Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

Biochemical changes in low-salt solid-state fermented soy sauce

(2016) Yanfang Zhang   AFRICAN JOURNAL OF BIOTECHNOLOGY

MDC-Analyzer: A novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites

(2016) Lixia Tang et al.   BIOTECHNIQUES

What would be the observable consequences if phospholipid bilayer diffusion of drugs into cells is negligible?

(2015) Douglas B. Kell   TRENDS IN PHARMACOLOGICAL SCIENCES

One in a Million: Flow Cytometric Sorting of Single Cell-Lysate Assays in Monodisperse Picolitre Double Emulsion Droplets for Directed Evolution

(2014) Anastasia Zinchenko et al.   ANALYTICAL CHEMISTRY

New Generation of Biocatalysts for Organic Synthesis

(2014) Bettina M. Nestl et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Organic Chemistry as a Language and the Implications of Chemical Linguistics for Structural and Retrosynthetic Analyses

(2014) Andrea Cadeddu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Gene and Protein Sequence Optimization for High-Level Production of Fully Active and Aglycosylated Lysostaphin in Pichia pastoris

(2014) H. Zhao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Directed evolution of nitrobenzene dioxygenase for the synthesis of the antioxidant hydroxytyrosol

(2014) Kalia Bernath-Levin et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

(2014) Kevin M Bradley et al.   Beilstein Journal of Organic Chemistry

CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

(2014) C. W. Wood et al.   BIOINFORMATICS

Engineering strictosidine synthase: Rational design of a small, focused circular permutation library of the β-propeller fold enzyme

(2014) Eva Fischereder et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Lessons from diversity of directed evolution experiments by an analysis of 3,000 mutations

(2014) Jing Zhao et al.   BIOTECHNOLOGY AND BIOENGINEERING

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility

(2014) Tsun-Tsao Huang et al.   BMC EVOLUTIONARY BIOLOGY

Computational Library Design for Increasing Haloalkane Dehalogenase Stability

(2014) Robert J. Floor et al.   CHEMBIOCHEM

Active Site Plasticity of a Computationally Designed Retro-Aldolase Enzyme

(2014) Richard Obexer et al.   ChemCatChem

CH-activating oxidative hydroxylation of 1-tetralones and related compounds with high regio- and stereoselectivity

(2014) Gheorghe-Doru Roiban et al.   CHEMICAL COMMUNICATIONS

Catalytic control in terpenoid cyclases: multiscale modeling of thermodynamic, kinetic, and dynamic effects

(2014) Dan Thomas Major et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Metalloenzyme design and engineering through strategic modifications of native protein scaffolds

(2014) Igor D Petrik et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

De novo protein components for oxidoreductase assembly and biological integration

(2014) Daniel W Watkins et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

New developments in ‘ene’-reductase catalysed biological hydrogenations

(2014) Helen S Toogood et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Recent achievements in developing the biocatalytic toolbox for chiral amine synthesis

(2014) Hannes Kohls et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Artificial metalloenzymes for enantioselective catalysis

(2014) Jeffrey Bos et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Recent achievments in the design and engineering of artificial metalloenzymes

(2014) Marc Dürrenberger et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Heavy enzymes—experimental and computational insights in enzyme dynamics

(2014) Katarzyna Świderek et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Protein engineering for development of new hydrolytic biocatalysts

(2014) Mikael Widersten   CURRENT OPINION IN CHEMICAL BIOLOGY

The role of reorganization energy in rational enzyme design

(2014) Monika Fuxreiter et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Computational tools for designing and engineering enzymes

(2014) Jiri Damborsky et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Engineering aldolases as biocatalysts

(2014) Claire L Windle et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Computer aided enzyme design and catalytic concepts

(2014) Maria P Frushicheva et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

HDX-MS guided drug discovery: small molecules and biopharmaceuticals

(2014) David P Marciano et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The emerging age of cell-free synthetic biology

(2014) Mark Thomas Smith et al.   FEBS LETTERS

Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations

(2014) Hein J. Wijma et al.   Journal of Chemical Information and Modeling

A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring

(2014) Sarah Sirin et al.   Journal of Chemical Information and Modeling

Spaces of the possible: universal Darwinism and the wall between technological and biological innovation

(2014) A. Wagner et al.   Journal of the Royal Society Interface

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

(2014) Miguel A. Campodonico et al.   METABOLIC ENGINEERING

Serum ferritin is an important inflammatory disease marker, as it is mainly a leakage product from damaged cells

(2014) Douglas B. Kell et al.   Metallomics

Identification of a novel ATP-binding cassette transporter involved in long-chain fatty acid import and its role in triacylglycerol accumulation in Rhodococcus jostii RHA1

(2014) M. S. Villalba et al.   MICROBIOLOGY-SGM

Review and analysis of performance metrics of droplet microfluidics systems

(2014) Liat Rosenfeld et al.   Microfluidics and Nanofluidics

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

(2014) Michal Galdzicki et al.   NATURE BIOTECHNOLOGY

New recipes for biocatalysis

(2014) Eric M Brustad   Nature Chemical Biology

The solute carrier SLC35F2 enables YM155-mediated DNA damage toxicity

(2014) Georg E Winter et al.   Nature Chemical Biology

Dynamics and hydration explain failed functional transformation in dehalogenase design

(2014) Jan Sykora et al.   Nature Chemical Biology

Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase

(2014) Megan L Matthews et al.   Nature Chemical Biology

The role of distant mutations and allosteric regulation on LovD active site dynamics

(2014) Gonzalo Jiménez-Osés et al.   Nature Chemical Biology

An orthogonal DNA replication system in yeast

(2014) Arjun Ravikumar et al.   Nature Chemical Biology

Evolution of enzyme catalysts caged in biomimetic gel-shell beads

(2014) Martin Fischlechner et al.   Nature Chemistry

A protein engineered to bind uranyl selectively and with femtomolar affinity

(2014) Lu Zhou et al.   Nature Chemistry

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser

(2014) David Arnlund et al.   NATURE METHODS

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Measuring the activity of protein variants on a large scale using deep mutational scanning

(2014) Douglas M Fowler et al.   Nature Protocols

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Realizing the potential of synthetic biology

(2014) George M. Church et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

GeneGenie: optimized oligomer design for directed evolution

(2014) Neil Swainston et al.   NUCLEIC ACIDS RESEARCH

An Improved Single Cell Ultrahigh Throughput Screening Method Based on In Vitro Compartmentalization

(2014) Fuqiang Ma et al.   PLoS One

De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

(2014) Tomasz Kosciolek et al.   PLoS One

A Rapid and Simple Method for DNA Engineering Using Cycled Ligation Assembly

(2014) Theodore L. Roth et al.   PLoS One

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

(2014) N. Preiswerk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution

(2014) Andrew Currin et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Computational design of water-soluble α-helical barrels

(2014) Andrew R. Thomson et al.   SCIENCE

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

Interfacing picoliter droplet microfluidics with addressable microliter compartments using fluorescence activated cell sorting

(2014) Yunpeng Bai et al.   SENSORS AND ACTUATORS B-CHEMICAL

Influence of Domain Interactions on Conformational Mobility of the Progesterone Receptor Detected by Hydrogen/Deuterium Exchange Mass Spectrometry

(2014) Devrishi Goswami et al.   STRUCTURE

Metalloprotein mimics – old tools in a new light

(2014) Thomas Happe et al.   TRENDS IN BIOTECHNOLOGY

Mutation rate plasticity in rifampicin resistance depends on Escherichia coli cell–cell interactions

(2014) Rok Krašovec et al.   Nature Communications

Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase

(2014) Nicole G. H. Leferink et al.   Nature Communications

On the validity versus utility of activity landscapes: are all activity cliffs statistically significant?

(2014) Rajarshi Guha et al.   Journal of Cheminformatics

Identification and use of an alkane transporter plug-in for applications in biocatalysis and whole-cell biosensing of alkanes

(2014) Chris Grant et al.   Scientific Reports

Proposed Data Model for the Next Version of the Synthetic Biology Open Language

(2014) Nicholas Roehner et al.   ACS Synthetic Biology

Rapid and Reliable DNA Assembly via Ligase Cycling Reaction

(2014) Stefan de Kok et al.   ACS Synthetic Biology

Speeding up Directed Evolution: Combining the Advantages of Solid-Phase Combinatorial Gene Synthesis with Statistically Guided Reduction of Screening Effort

(2014) Sabrina Hoebenreich et al.   ACS Synthetic Biology

Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution

(2014) Lizhi Ian Gong et al.   PLoS Genetics

How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion

(2014) Douglas B. Kell et al.   Frontiers in Pharmacology

Ultrarapid Generation of Femtoliter Microfluidic Droplets for Single-Molecule-Counting Immunoassays

(2013) Jung-uk Shim et al.   ACS Nano

The Evolution of an Amine Dehydrogenase Biocatalyst for the Asymmetric Production of Chiral Amines

(2013) Michael J. Abrahamson et al.   ADVANCED SYNTHESIS & CATALYSIS

Sensitive, High Throughput Detection of Proteins in Individual, Surfactant-Stabilized Picoliter Droplets Using Nanoelectrospray Ionization Mass Spectrometry

(2013) Clive A. Smith et al.   ANALYTICAL CHEMISTRY

Enzyme Promiscuity: Using a P450 Enzyme as a Carbene Transfer Catalyst

(2013) Gheorghe-Doru Roiban et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Importance of Additive and Non-Additive Mutational Effects in Protein Engineering

(2013) Manfred T. Reetz   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

High-Throughput Screening for Terpene-Synthase-Cyclization Activity and Directed Evolution of a Terpene Synthase

(2013) Ryan Lauchli et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Design of Protein Catalysts

(2013) Donald Hilvert   Annual Review of Biochemistry

SATP (YaaH), a succinate–acetate transporter protein inEscherichia coli

(2013) Joana Sá-Pessoa et al.   BIOCHEMICAL JOURNAL

Site-Directed Mutagenesis Maps Interactions That Enhance Cognate and Limit Promiscuous Catalysis by an Alkaline Phosphatase Superfamily Phosphodiesterase

(2013) Helen Wiersma-Koch et al.   BIOCHEMISTRY

A Population-Based Experimental Model for Protein Evolution: Effects of Mutation Rate and Selection Stringency on Evolutionary Outcomes

(2013) Aaron M. Leconte et al.   BIOCHEMISTRY

Aquaporins and membrane diffusion of CO2 in living organisms

(2013) Ralf Kaldenhoff et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Fatty acid transporters in skin development, function and disease

(2013) Meei-Hua Lin et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree

(2013) Andrew D. Moore et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Optimization of reorganization energy drives evolution of the designed Kemp eliminase KE07

(2013) A. Labas et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

APoc: large-scale identification of similar protein pockets

(2013) Mu Gao et al.   BIOINFORMATICS

Polishing the craft of genetic diversity creation in directed evolution

(2013) Kang Lan Tee et al.   BIOTECHNOLOGY ADVANCES

Stabilization of enzymes in ionic liquids via modification of enzyme charge

(2013) Erik M. Nordwald et al.   BIOTECHNOLOGY AND BIOENGINEERING

Transcriptome response to alkane biofuels in Saccharomyces cerevisiae: identification of efflux pumps involved in alkane tolerance

(2013) Hua Ling et al.   Biotechnology for Biofuels

Transporter engineering for improved tolerance against alkane biofuels in Saccharomyces cerevisiae

(2013) Binbin Chen et al.   Biotechnology for Biofuels

Directed evolution of an E. coli inner membrane transporter for improved efflux of biofuel molecules

(2013) Jee Foo et al.   Biotechnology for Biofuels

Directed evolution of cytochrome P450 for sterol epoxidation

(2013) Dan Jiang et al.   BIOTECHNOLOGY LETTERS

Flexibility and Reactivity in Promiscuous Enzymes

(2013) Pietro Gatti-Lafranconi et al.   CHEMBIOCHEM

Recent Advances in the Study of Enzyme Promiscuity in the Tautomerase Superfamily

(2013) Bert-Jan Baas et al.   CHEMBIOCHEM

Promiscuous Catalysis of Asymmetric Michael-Type Additions of Linear Aldehydes to β-Nitrostyrene by the Proline-Based Enzyme 4-Oxalocrotonate Tautomerase

(2013) Yufeng Miao et al.   CHEMBIOCHEM

Directed Evolution by Using Iterative Saturation Mutagenesis Based on Multiresidue Sites

(2013) Loreto P. Parra et al.   CHEMBIOCHEM

Activity Cliffs: Facts or Artifacts?

(2013) José L. Medina-Franco   Chemical Biology & Drug Design

Functionalizing Nanoparticles with Biological Molecules: Developing Chemistries that Facilitate Nanotechnology

(2013) Kim E. Sapsford et al.   CHEMICAL REVIEWS

Whole-cell biocatalysis for selective and productive C–O functional group introduction and modification

(2013) Manfred Schrewe et al.   CHEMICAL SOCIETY REVIEWS

Blood Tolerant Laccase by Directed Evolution

(2013) Diana M. Mate et al.   CHEMISTRY & BIOLOGY

The evolutionary ecology of technological innovations

(2013) Ricard V. Solée et al.   COMPLEXITY

Meta-omic characterization of prokaryotic gene clusters for natural product biosynthesis

(2013) Michael M Schofield et al.   CURRENT OPINION IN BIOTECHNOLOGY

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

(2013) Hans-Jörg Frasch et al.   CURRENT OPINION IN BIOTECHNOLOGY

Accelerated protein engineering for chemical biotechnology via homologous recombination

(2013) Erik M. Nordwald et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pathway and protein engineering approaches to produce novel and commodity small molecules

(2013) Namita Bhan et al.   CURRENT OPINION IN BIOTECHNOLOGY

Membrane proteins by accident or design

(2013) John Simms et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

New designed protein assemblies

(2013) Sabina Božič et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

De novo enzymes by computational design

(2013) Hajo Kries et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Biocatalysis enters a new era

(2013) Nicholas J Turner et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Innovation by homologous recombination

(2013) Devin L Trudeau et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

On the development of new biocatalytic processes for practical pharmaceutical synthesis

(2013) Gjalt W Huisman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Strategies for the discovery and engineering of enzymes for biocatalysis

(2013) Timo Davids et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Engineering and application of P450 monooxygenases in pharmaceutical and metabolite synthesis

(2013) Jill M Caswell et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

New approaches for sensing metabolites and proteins in live cells using RNA

(2013) Rita L Strack et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Computational protein design of ligand binding and catalysis

(2013) Kaspar Feldmeier et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Phosphorescence bioimaging using cyclometalated Ir(III) complexes

(2013) Youngmin You   CURRENT OPINION IN CHEMICAL BIOLOGY

Structure- and sequence-analysis inspired engineering of proteins for enhanced thermostability

(2013) Hein J Wijma et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

(2013) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Relating localized protein motions to the reaction coordinate in coenzyme B12-dependent enzymes

(2013) Alex R. Jones et al.   FEBS Journal

To get what we aim for - progress in diversity generation methods

(2013) Anna J. Ruff et al.   FEBS Journal

Characterizing rapid, activity-linked conformational transitions in proteins via sub-second hydrogen deuterium exchange mass spectrometry

(2013) Diana Resetca et al.   FEBS Journal

Computational design gains momentum in enzyme catalysis engineering

(2013) Hein J. Wijma et al.   FEBS Journal

Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it

(2013) Douglas B. Kell   FEBS Journal

Reporter-based screening and selection of enzymes

(2013) Teunke van Rossum et al.   FEBS Journal

Modulating protein stability - directed evolution strategies for improved protein function

(2013) Raymond D. Socha et al.   FEBS Journal

ABC transporters and cell wall proteins involved in organic solvent tolerance in Saccharomyces cerevisiae

(2013) Nao Nishida et al.   JOURNAL OF BIOTECHNOLOGY

Multi-site saturation by OmniChange yields a pH- and thermally improved phytase

(2013) Amol V. Shivange et al.   JOURNAL OF BIOTECHNOLOGY

Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function

(2013) Christopher Pfleger et al.   Journal of Chemical Information and Modeling

Recent Progress in Understanding Activity Cliffs and Their Utility in Medicinal Chemistry

(2013) Dagmar Stumpfe et al.   JOURNAL OF MEDICINAL CHEMISTRY

Janus: Prediction and Ranking of Mutations Required for Functional Interconversion of Enzymes

(2013) Trevor A. Addington et al.   JOURNAL OF MOLECULAR BIOLOGY

What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs

(2013) Eynat Dellus-Gur et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantum Mechanical/Molecular Mechanical Study on the Enantioselectivity of the Enzymatic Baeyer–Villiger Reaction of 4-Hydroxycyclohexanone

(2013) Iakov Polyak et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mediating Electrostatic Binding of 1-Butyl-3-methylimidazolium Chloride to Enzyme Surfaces Improves Conformational Stability

(2013) Erik M. Nordwald et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biocatalysis in Organic Chemistry and Biotechnology: Past, Present, and Future

(2013) Manfred T. Reetz   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Improved Biocatalysts from a Synthetic Circular Permutation Library of the Flavin-Dependent Oxidoreductase Old Yellow Enzyme

(2013) Ashley B. Daugherty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineering an Enantioselective Amine Oxidase for the Synthesis of Pharmaceutical Building Blocks and Alkaloid Natural Products

(2013) Diego Ghislieri et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ultrahigh-throughput sorting of microfluidic drops with flow cytometry

(2013) Shaun W. Lim et al.   LAB ON A CHIP

High-throughput screening for industrial enzyme production hosts by droplet microfluidics

(2013) Staffan L. Sjostrom et al.   LAB ON A CHIP

Challenges and pitfalls of P450-dependent (+)-valencene bioconversion by Saccharomyces cerevisiae

(2013) Carole Gavira et al.   METABOLIC ENGINEERING

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

(2013) Neil Swainston et al.   Metabolomics

Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure

(2013) So-Wei Yeh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recent advances in the heterologous expression of microbial natural product biosynthetic pathways

(2013) Sarah E. Ongley et al.   NATURAL PRODUCT REPORTS

Elucidation of the Fe(iv)=O intermediate in the catalytic cycle of the halogenase SyrB2

(2013) Shaun D. Wong et al.   NATURE

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

Catalytic conversion of nitrogen to ammonia by an iron model complex

(2013) John S. Anderson et al.   NATURE

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Biocatalytic retrosynthesis

(2013) Nicholas J Turner et al.   Nature Chemical Biology

Evolution of a designed retro-aldolase leads to complete active site remodeling

(2013) Lars Giger et al.   Nature Chemical Biology

Elementary tetrahelical protein design for diverse oxidoreductase functions

(2013) Tammer A Farid et al.   Nature Chemical Biology

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Pinocembrin protects brain against ischemia/reperfusion injury by attenuating endoplasmic reticulum stress induced apoptosis

(2013) Cai-xia Wu et al.   NEUROSCIENCE LETTERS

The Structure–Function Linkage Database

(2013) Eyal Akiva et al.   NUCLEIC ACIDS RESEARCH

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

Unusual properties of the cytochrome P450 superfamily

(2013) D. C. Lamb et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us?

(2013) S. L. Kelly et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An evolutionary framework for cultural change: Selectionism versus communal exchange

(2013) Liane Gabora   Physics of Life Reviews

Metabolic engineering and in vitro biosynthesis of phytochemicals and non-natural analogues

(2013) Mauricio Mora-Pale et al.   PLANT SCIENCE

Fitness Loss and Library Size Determination in Saturation Mutagenesis

(2013) Yuval Nov   PLoS One

Improving Glyphosate Oxidation Activity of Glycine Oxidase from Bacillus cereus by Directed Evolution

(2013) Tao Zhan et al.   PLoS One

Long-range protein-water dynamics in hyperactive insect antifreeze proteins

(2013) K. Meister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive experimental fitness landscape and evolutionary network for small RNA

(2013) J. I. Jimenez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transporter-mediated biofuel secretion

(2013) R. Doshi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-level description of ubiquitin folding

(2013) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dead-end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility

(2013) Mark A. Hallen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

(2013) Debswapna Bhattacharya et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

On the relationship between the sequence conservation and the packing density profiles of the protein complexes

(2013) Chih-Min Chang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evolution of Mammalian Diving Capacity Traced by Myoglobin Net Surface Charge

(2013) S. Mirceta et al.   SCIENCE

Root Effect Hemoglobin May Have Evolved to Enhance General Tissue Oxygen Delivery

(2013) J. L. Rummer et al.   SCIENCE

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

(2013) C. Natarajan et al.   SCIENCE

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

Protein Modeling: What Happened to the “Protein Structure Gap”?

(2013) Torsten Schwede   STRUCTURE

Laccase-mediated oxidation of small organics: bifunctional roles for versatile applications

(2013) Jong-Rok Jeon et al.   TRENDS IN BIOTECHNOLOGY

Substrate promiscuity of cytochrome P450 RhF

(2013) Elaine O'Reilly et al.   Catalysis Science & Technology

Enzyme engineering toolbox – a ‘catalyst’ for change

(2013) Helen S. Toogood et al.   Catalysis Science & Technology

Cell-free Protein Synthesis in a Microchamber Revealed the Presence of an Optimum Compartment Volume for High-order Reactions

(2013) Taiji Okano et al.   ACS Synthetic Biology

Orthogonal Riboswitches for Tuneable Coexpression in Bacteria

(2012) Neil Dixon et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Reprogramming the Genetic Code: From Triplet to Quadruplet Codes

(2012) Kaihang Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Redox Self-Sufficient Biocatalyst Network for the Amination of Primary Alcohols

(2012) Johann H. Sattler et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Development of an Amine Dehydrogenase for Synthesis of Chiral Amines

(2012) Michael J. Abrahamson et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Quantitative Imaging with Fluorescent Biosensors

(2012) Sakiko Okumoto et al.   Annual Review of Plant Biology

Regio- and stereoselective oxidation of unactivated C–H bonds withRhodococcus rhodochrous

(2012) Elaine O’Reilly et al.   Beilstein Journal of Organic Chemistry

Intrinsic disorder in proteins: a challenge for (un)structural biology met by ion mobility–mass spectrometry

(2012) Ewa Jurneczko et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Engineering oxidoreductases: maquette proteins designed from scratch

(2012) Bruce R. Lichtenstein et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Reconstructing a Missing Link in the Evolution of a Recently Diverged Phosphotriesterase by Active-Site Loop Remodeling

(2012) Livnat Afriat-Jurnou et al.   BIOCHEMISTRY

Analysis of the local dynamics of human insulin and a rapid-acting insulin analog by hydrogen/deuterium exchange mass spectrometry

(2012) Shiori Nakazawa et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer

(2012) Mark F. Mohamed et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Scientific discovery as a combinatorial optimisation problem: How best to navigate the landscape of possible experiments?

(2012) Douglas B. Kell   BIOESSAYS

Measuring and comparing structural fluctuation patterns in large protein datasets

(2012) Edvin Fuglebakk et al.   BIOINFORMATICS

Bet-hedging-a triple trade-off between means, variances and correlations

(2012) Jostein Starrfelt et al.   BIOLOGICAL REVIEWS

Biocatalyst development by directed evolution

(2012) Meng Wang et al.   BIORESOURCE TECHNOLOGY

Software tools for identification, visualization and analysis of protein tunnels and channels

(2012) Jan Brezovsky et al.   BIOTECHNOLOGY ADVANCES

Algorithms for optimizing cross-overs in DNA shuffling

(2012) Lu He et al.   BMC BIOINFORMATICS

EnzML: multi-label prediction of enzyme classes using InterPro signatures

(2012) Luna De Ferrari et al.   BMC BIOINFORMATICS

Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast

(2012) Karin Lanthaler et al.   BMC BIOLOGY

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Directed Evolution of Highly Selective Proteases by Using a Novel FACS-Based Screen that Capitalizes on the p53 Regulator MDM2

(2012) Tae Hyeon Yoo et al.   CHEMBIOCHEM

Directed Evolution of the Enzyme Monoamine Oxidase (MAO-N): Highly Efficient Chemo-enzymatic Deracemisation of the Alkaloid (±)-Crispine A

(2012) Ian Rowles et al.   ChemCatChem

Radiometals for Combined Imaging and Therapy

(2012) Cathy S. Cutler et al.   CHEMICAL REVIEWS

Deep eutectic solvents: syntheses, properties and applications

(2012) Qinghua Zhang et al.   CHEMICAL SOCIETY REVIEWS

Picoliter Cell Lysate Assays in Microfluidic Droplet Compartments for Directed Enzyme Evolution

(2012) Balint Kintses et al.   CHEMISTRY & BIOLOGY

Evolution in Microfluidic Droplet

(2012) Itay Levin et al.   CHEMISTRY & BIOLOGY

Enhancing the Efficiency of Directed Evolution in Focused Enzyme Libraries by the Adaptive Substituent Reordering Algorithm

(2012) Xiaojiang Feng et al.   CHEMISTRY-A EUROPEAN JOURNAL

Protein Engineering of Stereoselective Baeyer-Villiger Monooxygenases

(2012) Zhi-Gang Zhang et al.   CHEMISTRY-A EUROPEAN JOURNAL

Peptides as complexing agents: Factors influencing the structure and thermodynamic stability of peptide complexes

(2012) Imre Sóvágó et al.   COORDINATION CHEMISTRY REVIEWS

Directed evolution: tailoring biocatalysts for industrial applications

(2012) Ashwani Kumar et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

A retrosynthetic biology approach to therapeutics: from conception to delivery

(2012) Anne-Gaëlle Planson et al.   CURRENT OPINION IN BIOTECHNOLOGY

Systems and synthetic metabolic engineering for amino acid production – the heartbeat of industrial strain development

(2012) Judith Becker et al.   CURRENT OPINION IN BIOTECHNOLOGY

DNA synthesis, assembly and applications in synthetic biology

(2012) Siying Ma et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Directed enzyme evolution: beyond the low-hanging fruit

(2012) Moshe Goldsmith et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

(2012) Peter Csermely et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so

(2012) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Catalytic promiscuity inPseudomonas aeruginosaarylsulfatase as an example of chemistry-driven protein evolution

(2012) Jinghui Luo et al.   FEBS LETTERS

Sequence-function-stability relationships in proteins from datasets of functionally annotated variants: The case of TEM β-lactamases

(2012) Luciano A. Abriata et al.   FEBS LETTERS

Rates and Fitness Consequences of New Mutations in Humans

(2012) Peter D. Keightley   GENETICS

QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization

(2012) Stephanus Daniel Handoko et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Internal friction in enzyme reactions

(2012) Anna Rauscher et al.   IUBMB LIFE

Identification of Transport Proteins Involved in Free Fatty Acid Efflux in Escherichia coli

(2012) R. M. Lennen et al.   JOURNAL OF BACTERIOLOGY

Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio

(2012) Prakash C. Rathi et al.   JOURNAL OF BIOTECHNOLOGY

Computational biotechnology: Prediction of competitive substrate inhibition of enzymes by buffer compounds with protein–ligand docking

(2012) Karen T. Schomburg et al.   JOURNAL OF BIOTECHNOLOGY

Improved thermostability of AEH by combining B-FIT analysis and structure-guided consensus method

(2012) Janna K. Blum et al.   JOURNAL OF BIOTECHNOLOGY

Frequency of Occurrence and Potency Range Distribution of Activity Cliffs in Bioactive Compounds

(2012) Dagmar Stumpfe et al.   Journal of Chemical Information and Modeling

Exploring Uncharted Territories: Predicting Activity Cliffs in Structure–Activity Landscapes

(2012) Rajarshi Guha   Journal of Chemical Information and Modeling

MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement

(2012) Paulette A. Greenidge et al.   Journal of Chemical Information and Modeling

FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach

(2012) Hongyi Zhou et al.   Journal of Chemical Information and Modeling

Global and local indices for characterizing biomolecular flexibility and rigidity

(2012) Christopher Pfleger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

(2012) Matthew P. Repasky et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Multiple ligand docking by Glide: implications for virtual second-site screening

(2012) Márton Vass et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Exploring Activity Cliffs in Medicinal Chemistry

(2012) Dagmar Stumpfe et al.   JOURNAL OF MEDICINAL CHEMISTRY

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

(2012) Christophe Schmitz et al.   JOURNAL OF MOLECULAR BIOLOGY

Combinatorial Design of an Anticalin Directed against the Extra-Domain B for the Specific Targeting of Oncofetal Fibronectin

(2012) Michaela Gebauer et al.   JOURNAL OF MOLECULAR BIOLOGY

Evaluation and Optimization of Discrete State Models of Protein Folding

(2012) Elizabeth H. Kellogg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Pressure Effects on Enzyme-Catalyzed Quantum Tunneling Events Arise from Protein-Specific Structural and Dynamic Changes

(2012) Sam Hay et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Influence of Fluorination on the Thermodynamics of Protein Folding

(2012) Benjamin C. Buer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Potential of Fragment Recombination for Rational Design of Proteins

(2012) Simone Eisenbeis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Design of an α-Gliadin Peptidase

(2012) Sydney R. Gordon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Induced Axial Chirality in Biocatalytic Asymmetric Ketone Reduction

(2012) Rubén Agudo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cell-free protein synthesis from a single copy of DNA in a glass microchamber

(2012) Taiji Okano et al.   LAB ON A CHIP

A disposable picolitre bioreactor for cultivation and investigation of industrially relevant bacteria on the single cell level

(2012) Alexander Grünberger et al.   LAB ON A CHIP

A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution

(2012) Ali Fallah-Araghi et al.   LAB ON A CHIP

Cell-Free Protein Synthesis inside Giant Unilamellar Vesicles Analyzed by Flow Cytometry

(2012) Koji Nishimura et al.   LANGMUIR

Metabolic engineering of Escherichia coli for (2S)-pinocembrin production from glucose by a modular metabolic strategy

(2012) Junjun Wu et al.   METABOLIC ENGINEERING

In vitro selection of proteins via emulsion compartments

(2012) Wei-Cheng Lu et al.   METHODS

A compendium of inborn errors of metabolism mapped onto the human metabolic network

(2012) Swagatika Sahoo et al.   Molecular BioSystems

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis

(2012) Fernando Geu-Flores et al.   NATURE

High-valent organometallic copper and palladium in catalysis

(2012) Amanda J. Hickman et al.   NATURE

Engineering the third wave of biocatalysis

(2012) U. T. Bornscheuer et al.   NATURE

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

The expanding scope of DNA sequencing

(2012) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

(2012) Christopher B Eiben et al.   NATURE BIOTECHNOLOGY

A metalloenzyme reloaded

(2012) Birte Höcker   Nature Chemical Biology

Metallo-β-lactamases withstand low Zn(II) conditions by tuning metal-ligand interactions

(2012) Javier M González et al.   Nature Chemical Biology

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

(2012) Sagar D Khare et al.   Nature Chemical Biology

Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins

(2012) Amanda J. Reig et al.   Nature Chemistry

Good vibrations in enzyme-catalysed reactions

(2012) Sam Hay et al.   Nature Chemistry

Biosynthesis of luminescent quantum dots in an earthworm

(2012) S. R. Stürzenbaum et al.   Nature Nanotechnology

Significance of Short Chain Fatty Acid Transport by Members of the Monocarboxylate Transporter Family (MCT)

(2012) Ivano Moschen et al.   NEUROCHEMICAL RESEARCH

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

(2012) Tony E. Lewis et al.   NUCLEIC ACIDS RESEARCH

‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules

(2012) Hwangbeom Kim et al.   NUCLEIC ACIDS RESEARCH

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

(2012) Ida Schomburg et al.   NUCLEIC ACIDS RESEARCH

Rational substrate and enzyme engineering of transketolase for aromatics

(2012) Panwajee Payongsri et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

The Eight Criteria Defining a Good Chemical Manufacturing Process

(2012) Rolf Dach et al.   ORGANIC PROCESS RESEARCH & DEVELOPMENT

Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses

(2012) J E Jimenez-Roldan et al.   PHYSICAL BIOLOGY

Quantitative imaging using genetically encoded sensors for small molecules in plants

(2012) Sakiko Okumoto   PLANT JOURNAL

Directed Evolution of the Transcriptional Regulator DntR: Isolation of Mutants with Improved DNT-Response

(2012) Rosa Lönneborg et al.   PLoS One

A Unified Multitask Architecture for Predicting Local Protein Properties

(2012) Yanjun Qi et al.   PLoS One

An Automated Flow for Directed Evolution Based on Detection of Promiscuous Scaffolds Using Spatial and Electrostatic Properties of Catalytic Residues

(2012) Sandeep Chakraborty   PLoS One

Improving Lambda Red Genome Engineering in Escherichia coli via Rational Removal of Endogenous Nucleases

(2012) Joshua A. Mosberg et al.   PLoS One

Exploiting Genomic Knowledge in Optimising Molecular Breeding Programmes: Algorithms from Evolutionary Computing

(2012) Steve O'Hagan et al.   PLoS One

Exploring Sequence Characteristics Related to High-Level Production of Secreted Proteins in Aspergillus niger

(2012) Bastiaan A. van den Berg et al.   PLoS One

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

(2012) T. Nugent et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates

(2012) R. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

(2012) T. Lukk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for the enhanced stability of highly fluorinated proteins

(2012) B. C. Buer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictability of evolution depends nonmonotonically on population size

(2012) I. G. Szendro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

(2012) O. F. Lange et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Iterative approach to computational enzyme design

(2012) H. K. Privett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

(2012) O. Khersonsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drift-barrier hypothesis and mutation-rate evolution

(2012) W. Sung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Directed evolution of the peroxidase activity of a de novo-designed protein

(2012) S. C. Patel et al.   PROTEIN ENGINEERING DESIGN & SELECTION

TRINS: a method for gene modification by randomized tandem repeat insertions

(2012) Y. Kipnis et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Multistate approaches in computational protein design

(2012) James A. Davey et al.   PROTEIN SCIENCE

Comparison of designed and randomly generated catalysts for simple chemical reactions

(2012) Yakov Kipnis et al.   PROTEIN SCIENCE

Robust design and optimization of retroaldol enzymes

(2012) Eric A. Althoff et al.   PROTEIN SCIENCE

Fluorine: A new element in protein design

(2012) Benjamin C. Buer et al.   PROTEIN SCIENCE

Chimeragenesis of distantly-related proteins by noncontiguous recombination

(2012) Matthew A. Smith et al.   PROTEIN SCIENCE

Evolutionary information hidden in a single protein structure

(2012) Chien-Hua Shih et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Achieving Diversity in the Face of Constraints: Lessons from Metabolism

(2012) R. Milo et al.   SCIENCE

Fluorescence Imaging of Cellular Metabolites with RNA

(2012) Jeremy S. Paige et al.   SCIENCE

Reprogramming the Genetic Code

(2012) J. W. Chin   SCIENCE

Oxidative Aliphatic C-H Fluorination with Fluoride Ion Catalyzed by a Manganese Porphyrin

(2012) W. Liu et al.   SCIENCE

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Biotinylated Rh(III) Complexes in Engineered Streptavidin for Accelerated Asymmetric C-H Activation

(2012) T. K. Hyster et al.   SCIENCE

Broadly Neutralizing Antibodies Present New Prospects to Counter Highly Antigenically Diverse Viruses

(2012) D. R. Burton et al.   SCIENCE

Epistemic and methodological iteration in scientific research

(2012) Kevin C. Elliott   STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE

Practical separation of alcohol–ester mixtures using Deep-Eutectic-Solvents

(2012) Zaira Maugeri et al.   TETRAHEDRON LETTERS

Applications and perspectives of multi-parameter flow cytometry to microbial biofuels production processes

(2012) Teresa Lopes da Silva et al.   TRENDS IN BIOTECHNOLOGY

Genetic encoding of fluorescent RNA ensures a bright future for visualizing nucleic acid dynamics

(2012) Jason Dictenberg   TRENDS IN BIOTECHNOLOGY

Biotechnological opportunities with the β-ketoadipate pathway

(2012) Tyrone Wells et al.   TRENDS IN BIOTECHNOLOGY

Next generation deep sequencing and vaccine design: today and tomorrow

(2012) Fabio Luciani et al.   TRENDS IN BIOTECHNOLOGY

Engineering Escherichia coli to synthesize free fatty acids

(2012) Rebecca M. Lennen et al.   TRENDS IN BIOTECHNOLOGY

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

Exploring structure-activity data using the landscape paradigm

(2012) Rajarshi Guha   Wiley Interdisciplinary Reviews-Computational Molecular Science

SCHEMA-Designed Variants of Human Arginase I and II Reveal Sequence Elements Important to Stability and Catalysis

(2012) Philip A. Romero et al.   ACS Synthetic Biology

Reducing Codon Redundancy and Screening Effort of Combinatorial Protein Libraries Created by Saturation Mutagenesis

(2012) Sabrina Kille et al.   ACS Synthetic Biology

Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach

(2012) Hector Garcia-Seisdedos et al.   PLoS Computational Biology

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

(2012) Nicholas Furnham et al.   PLoS Computational Biology

A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level

(2012) Stephan Binder et al.   GENOME BIOLOGY

COMPUTER-AIDED PROTEIN DIRECTED EVOLUTION: A REVIEW OF WEB SERVERS, DATABASES AND OTHER COMPUTATIONAL TOOLS FOR PROTEIN ENGINEERING

(2012) Rajni Verma et al.   Computational and Structural Biotechnology Journal

DIRECTED EVOLUTION: SELECTION OF THE HOST ORGANISM

(2012) Azadeh Pourmir et al.   Computational and Structural Biotechnology Journal

RECENT ADVANCES IN RATIONAL APPROACHES FOR ENZYME ENGINEERING

(2012) Kerstin Steiner et al.   Computational and Structural Biotechnology Journal

Chemical Tags for Labeling Proteins Inside Living Cells

(2011) Chaoran Jing et al.   ACCOUNTS OF CHEMICAL RESEARCH

Engineering Transaldolase in Pichia stipitis to Improve Bioethanol Production

(2011) Shan-He Chen et al.   ACS Chemical Biology

Discovery and Protein Engineering of Biocatalysts for Organic Synthesis

(2011) Geoffrey A. Behrens et al.   ADVANCED SYNTHESIS & CATALYSIS

Rapid Formation of a Preoligomeric Peptide-Metal-Peptide Complex Following Copper(II) Binding to Amyloid β Peptides

(2011) Jeppe T. Pedersen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Tuning a P450 Enzyme for Methane Oxidation

(2011) Felipe E. Zilly et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Combination of In Vivo Selection and Cell Sorting for the Identification of Enantioselective Biocatalysts

(2011) Elena Fernández-Álvaro et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

In Vivo Incorporation of Multiple Noncanonical Amino Acids into Proteins

(2011) Michael G. Hoesl et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Theoretical and Computational Protein Design

(2011) Ilan Samish et al.   Annual Review of Physical Chemistry

Engineering Platforms for Directed Evolution of Laccase from Pycnoporus cinnabarinus

(2011) S. Camarero et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Chimeric self-sufficient P450cam-RhFRed biocatalysts with broad substrate scope

(2011) Aélig Robin et al.   Beilstein Journal of Organic Chemistry

Substrate specificity of haloalkane dehalogenases

(2011) Tana Koudelakova et al.   BIOCHEMICAL JOURNAL

Directed evolution of a temperature-, peroxide- and alkaline pH-tolerant versatile peroxidase

(2011) Eva Garcia-Ruiz et al.   BIOCHEMICAL JOURNAL

Challenges and Advances in Validating Enzyme Design Proposals: The Case of Kemp Eliminase Catalysis

(2011) Maria P. Frushicheva et al.   BIOCHEMISTRY

Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis

(2011) Gordon G. Hammes et al.   BIOCHEMISTRY

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Screening of marine microalgae for biodiesel feedstock

(2011) Thi Thai Yen Doan et al.   BIOMASS & BIOENERGY

Diverse role of conformational dynamics in carboxypeptidase A-driven peptide and ester hydrolyses: Disclosing the “Perfect Induced Fit” and “Protein Local Unfolding” pathways by altering protein stability

(2011) Mikhael Shushanyan et al.   BIOPOLYMERS

The imminent role of protein engineering in synthetic biology

(2011) Jee Loon Foo et al.   BIOTECHNOLOGY ADVANCES

2D format for screening bacterial cells at the throughput of flow cytometry

(2011) Alexander A. Gordeev et al.   BIOTECHNOLOGY AND BIOENGINEERING

Kinetic modeling of free fatty acid production in Escherichia coli based on continuous cultivation of a plasmid free strain

(2011) J. Tyler Youngquist et al.   BIOTECHNOLOGY AND BIOENGINEERING

Manipulation of enzyme properties by noncanonical amino acid incorporation

(2011) Shun Zheng et al.   Biotechnology Journal

Patch oligodeoxynucleotide synthesis (POS): a novel method for synthesis of long DNA sequences and full-length genes

(2011) Guanghua Yang et al.   BIOTECHNOLOGY LETTERS

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

(2011) Pablo Carbonell et al.   BMC Systems Biology

SeSaM-Tv-II Generates a Protein Sequence Space that is Unobtainable by epPCR

(2011) Hemanshu Mundhada et al.   CHEMBIOCHEM

An Efficient Route to Selective Bio-oxidation Catalysts: an Iterative Approach Comprising Modeling, Diversification, and Screening, Based on CYP102A1

(2011) Alexander Seifert et al.   CHEMBIOCHEM

Directed Evolution Strategies for Enantiocomplementary Haloalkane Dehalogenases: From Chemical Waste to Enantiopure Building Blocks

(2011) Jan G. E. van Leeuwen et al.   CHEMBIOCHEM

A Fast and Precise Approach for Computational Saturation Mutagenesis and its Experimental Validation by Using an Artificial (βα)8-Barrel Protein

(2011) Andre Fischer et al.   CHEMBIOCHEM

Enhancing the Thermal Robustness of an Enzyme by Directed Evolution: Least Favorable Starting Points and Inferior Mutants Can Map Superior Evolutionary Pathways

(2011) Yosephine Gumulya et al.   CHEMBIOCHEM

Stabilization of a Metabolic Enzyme by Library Selection in Thermus thermophilus

(2011) Thomas Schwab et al.   CHEMBIOCHEM

Lessons about Protein Stability from in vitro Selections

(2011) Franz-Xaver Schmid   CHEMBIOCHEM

Towards a Restriction Proteinase: Construction of a Self-Activating Enzyme

(2011) Michael Schöpfel et al.   CHEMBIOCHEM

The Transaldolase Family: New Synthetic Opportunities from an Ancient Enzyme Scaffold

(2011) Anne K. Samland et al.   CHEMBIOCHEM

Generation of Novel Nucleases with Extended Specificity by Rational and Combinatorial Strategies

(2011) Alfred Pingoud et al.   CHEMBIOCHEM

Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity

(2011) Samra Obeid et al.   CHEMBIOCHEM

Protein Engineering of α/β-Hydrolase Fold Enzymes

(2011) Helge Jochens et al.   CHEMBIOCHEM

A Library Approach for the Discovery of Customized Yeast Three-Hybrid Counter Selections

(2011) Laura M. Wingler et al.   CHEMBIOCHEM

A “Diels-Alderase” at Last

(2011) Craig A. Townsend   CHEMBIOCHEM

Colorimetric logic gates for small molecules using split/integrated aptamers and unmodified gold nanoparticles

(2011) Xiaowen Xu et al.   CHEMICAL COMMUNICATIONS

Artificial metalloenzymes for olefin metathesis based on the biotin-(strept)avidin technology

(2011) Cheikh Lo et al.   CHEMICAL COMMUNICATIONS

Application of Designed Enzymes in Organic Synthesis

(2011) Gernot A. Strohmeier et al.   CHEMICAL REVIEWS

Protein design in metabolic engineering and synthetic biology

(2011) Jürgen Pleiss   CURRENT OPINION IN BIOTECHNOLOGY

DARPins and other repeat protein scaffolds: advances in engineering and applications

(2011) Ykelien L Boersma et al.   CURRENT OPINION IN BIOTECHNOLOGY

Molecular design of the microbial cell surface toward the recovery of metal ions

(2011) Kouichi Kuroda et al.   CURRENT OPINION IN BIOTECHNOLOGY

Cytochrome P450: taming a wild type enzyme

(2011) Sang Taek Jung et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins

(2011) Jeffery G Saven   CURRENT OPINION IN CHEMICAL BIOLOGY

Novel proteins: from fold to function

(2011) Betsy A Smith et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Recent advances in computational protein design

(2011) Robert J Pantazes et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-based systems biology for analyzing off-target binding

(2011) Lei Xie et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Strategy and success for the directed evolution of enzymes

(2011) Paul A Dalby   CURRENT OPINION IN STRUCTURAL BIOLOGY

Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only

(2011) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Binding sites in membrane proteins – Diversity, druggability and prospects

(2011) Robert Adams et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Biocatalytic Promiscuity

(2011) Maria Svedendahl Humble et al.   EUROPEAN JOURNAL OF ORGANIC CHEMISTRY

VISUALIZING FITNESS LANDSCAPES

(2011) David M. McCandlish   EVOLUTION

BindingDB and ChEMBL: online compound databases for drug discovery

(2011) Anne Mai Wassermann et al.   Expert Opinion on Drug Discovery

Temperature dependence of internal friction in enzyme reactions

(2011) Anna Á. Rauscher et al.   FASEB JOURNAL

Molecular basis of glyphosate resistance - different approaches through protein engineering

(2011) Loredano Pollegioni et al.   FEBS Journal

Multiple Adaptive Substitutions During Evolution in Novel Environments

(2011) Kavita Jain et al.   GENETICS

Enzymatic reductions for the chemist

(2011) Frank Hollmann et al.   GREEN CHEMISTRY

Inference of Functional Properties from Large-scale Analysis of Enzyme Superfamilies

(2011) Shoshana D. Brown et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Origins of Specificity and Promiscuity in Metabolic Networks

(2011) Pablo Carbonell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Divergent Evolution in Enolase Superfamily: Strategies for Assigning Functions

(2011) John A. Gerlt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chemical tags: Applications in live cell fluorescence imaging

(2011) Richard Wombacher et al.   Journal of Biophotonics

Directed evolution to re-adapt a co-evolved network within an enzyme

(2011) John Strafford et al.   JOURNAL OF BIOTECHNOLOGY

Design of Multitarget Activity Landscapes That Capture Hierarchical Activity Cliff Distributions

(2011) Dilyana Dimova et al.   Journal of Chemical Information and Modeling

RASA: A Rapid Retrosynthesis-Based Scoring Method for the Assessment of Synthetic Accessibility of Drug-like Molecules

(2011) Qi Huang et al.   Journal of Chemical Information and Modeling

LigBuilder 2: A Practicalde NovoDrug Design Approach

(2011) Yaxia Yuan et al.   Journal of Chemical Information and Modeling

Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein−Ligand Complexes

(2011) John C. Faver et al.   Journal of Chemical Theory and Computation

Triosephosphate Isomerase by Consensus Design: Dramatic Differences in Physical Properties and Activity of Related Variants

(2011) Brandon J. Sullivan et al.   JOURNAL OF MOLECULAR BIOLOGY

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

(2011) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Directed Evolution of Sulfotransferases and Paraoxonases by Ancestral Libraries

(2011) Uria Alcolombri et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Analyses of Covalent Enzyme–Substrate Analog Complexes Reveal Strengths and Limitations of De Novo Enzyme Design

(2011) Ling Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

A Stereoselective Vanadium-Dependent Chloroperoxidase in Bacterial Antibiotic Biosynthesis

(2011) Peter Bernhardt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reengineering a Tryptophan Halogenase To Preferentially Chlorinate a Direct Alkaloid Precursor

(2011) Weslee S. Glenn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sequencing antibody repertoires

(2011) Nicolas Fischer   mAbs

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

Synthetic biology: New strategies for directing design

(2011) Sean A. Lynch et al.   METABOLIC ENGINEERING

Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler

(2011) Zengyi Shao et al.   Molecular BioSystems

A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function

(2011) Troy Wymore et al.   Molecular Informatics

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Controlled vocabularies and semantics in systems biology

(2011) M. Courtot et al.   Molecular Systems Biology

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

(2011) Guillaume Bouvignies et al.   NATURE

Enzyme-catalysed [4+2] cycloaddition is a key step in the biosynthesis of spinosyn A

(2011) Hak Joong Kim et al.   NATURE

Directed evolution of hydrolases for prevention of G-type nerve agent intoxication

(2011) Rinkoo D Gupta et al.   Nature Chemical Biology

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Crystal structure of a monomeric retroviral protease solved by protein folding game players

(2011) Firas Khatib et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Error correction of microchip synthesized genes using Surveyor nuclease

(2011) Ishtiaq Saaem et al.   NUCLEIC ACIDS RESEARCH

MACiE: exploring the diversity of biochemical reactions

(2011) Gemma L. Holliday et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Comparison of the Frequency of Functional SH3 Domains with Different Limited Sets of Amino Acids Using mRNA Display

(2011) Junko Tanaka et al.   PLoS One

De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth

(2011) Michael A. Fisher et al.   PLoS One

Modeling Symmetric Macromolecular Structures in Rosetta3

(2011) Frank DiMaio et al.   PLoS One

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

(2011) Sarel J. Fleishman et al.   PLoS One

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design

(2011) Colin A. Smith et al.   PLoS One

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Development of Non-Natural Flavanones as Antimicrobial Agents

(2011) Zachary L. Fowler et al.   PLoS One

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

OmniChange: The Sequence Independent Method for Simultaneous Site-Saturation of Five Codons

(2011) Alexander Dennig et al.   PLoS One

Molecular bases of thermophily in hyperthermophiles

(2011) Tadayuki IMANAKA   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library

(2011) A. G. Sandstrom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

(2011) A. J. Adamczyk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of epistasis and pleiotropy on evolutionary adaptation

(2011) B. Ostman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Engineering highly thermostable xylanase variants using an enhanced combinatorial library method

(2011) C. A. Hokanson et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Protein topology from predicted residue contacts

(2011) William R. Taylor et al.   PROTEIN SCIENCE

Computational design and selections for an engineered, thermostable terpene synthase

(2011) Juan E. Diaz et al.   PROTEIN SCIENCE

The dual role of fragments in fragment-assembly methods for de novo protein structure prediction

(2011) Julia Handl et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A divide-and-conquer approach to determine the Pareto frontier for optimization of protein engineering experiments

(2011) Lu He et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Incorporation of evolutionary information into Rosetta comparative modeling

(2011) James Thompson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis

(2011) G. Bhabha et al.   SCIENCE

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Surveying the Manifold Divergence of an Entire Protein Class for Statistical Clues to Underlying Biochemical Mechanisms

(2011) Andrew F. Neuwald   Statistical Applications in Genetics and Molecular Biology

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

Cytochrome P450 monooxygenases: an update on perspectives for synthetic application

(2011) Vlada B. Urlacher et al.   TRENDS IN BIOTECHNOLOGY

Biocatalysis: Synthesis of Key Intermediates for Development of Pharmaceuticals

(2011) Ramesh N. Patel   ACS Catalysis

Novel choline-chloride-based deep-eutectic-solvents with renewable hydrogen bond donors: levulinic acid and sugar-based polyols

(2011) Zaira Maugeri et al.   RSC Advances

Evolutionary Accessibility of Mutational Pathways

(2011) Jasper Franke et al.   PLoS Computational Biology

Switch of substrate specificity of hyperthermophilic acylaminoacyl peptidase by combination of protein and solvent engineering

(2011) Chang Liu et al.   Protein & Cell

Artificial Metalloenzymes Based on the Biotin−Avidin Technology: Enantioselective Catalysis and Beyond

(2010) Thomas R. Ward   ACCOUNTS OF CHEMICAL RESEARCH

Encapsulating Bacteria in Agarose Microparticles Using Microfluidics for High-Throughput Cell Analysis and Isolation

(2010) Ye-Jin Eun et al.   ACS Chemical Biology

Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

(2010) Zbynek Prokop et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions

(2010) Manfred T. Reetz   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry

High-Throughput Metabolic Engineering: Advances in Small-Molecule Screening and Selection

(2010) Jeffrey A. Dietrich et al.   Annual Review of Biochemistry

Adding New Chemistries to the Genetic Code

(2010) Chang C. Liu et al.   Annual Review of Biochemistry

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Product-Induced Gene Expression, a Product-Responsive Reporter Assay Used To Screen Metagenomic Libraries for Enzyme-Encoding Genes

(2010) T. Uchiyama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Production of recombinant proteins and metabolites in yeasts

(2010) Danilo Porro et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

New and classic families of secreted fungal heme peroxidases

(2010) Martin Hofrichter et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Single-cell analysis and isolation for microbiology and biotechnology: methods and applications

(2010) Satoshi Ishii et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson’s, Huntington’s, Alzheimer’s, prions, bactericides, chemical toxicology and others as examples

(2010) Douglas B. Kell   ARCHIVES OF TOXICOLOGY

Application of maximin correlation analysis to classifying protein environments for function prediction

(2010) Taehoon Lee et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution

(2010) Yumewo Suzuki et al.   BIOCHEMICAL JOURNAL

A convenient and robust method for construction of combinatorial and random mutant libraries

(2010) Yingfeng An et al.   BIOCHIMIE

Predictive models for population performance on real biological fitness landscapes

(2010) William Rowe et al.   BIOINFORMATICS

Molecular signatures-based prediction of enzyme promiscuity

(2010) Pablo Carbonell et al.   BIOINFORMATICS

Barrier Compression and Its Contribution to Both Classical and Quantum Mechanical Aspects of Enzyme Catalysis

(2010) Sam Hay et al.   BIOPHYSICAL JOURNAL

Molecular biomimetics: GEPI-based biological routes to technology

(2010) Candan Tamerler et al.   BIOPOLYMERS

The α/β-Hydrolase Fold 3DM Database (ABHDB) as a Tool for Protein Engineering

(2010) Robert Kourist et al.   CHEMBIOCHEM

Combinatorial Alanine Substitution Enables Rapid Optimization of Cytochrome P450BM3 for Selective Hydroxylation of Large Substrates

(2010) Jared C. Lewis et al.   CHEMBIOCHEM

Natural Diversity to Guide Focused Directed Evolution

(2010) Helge Jochens et al.   CHEMBIOCHEM

Biocatalytic Redox Reactions for Organic Synthesis: Nonconventional Regeneration Methods

(2010) Frank Hollmann et al.   ChemCatChem

Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method

(2010) Manfred T. Reetz et al.   CHEMICAL COMMUNICATIONS

Model for solvent viscosity effect on enzymatic reactions

(2010) A.E. Sitnitsky   CHEMICAL PHYSICS

Computational protein design, from single domain soluble proteins to membrane proteins

(2010) Pu Tian   CHEMICAL SOCIETY REVIEWS

Design, synthesis and biological application of chemical probes for bio-imaging

(2010) Kazuya Kikuchi   CHEMICAL SOCIETY REVIEWS

Hydrogen exchange mass spectrometry for studying protein structure and dynamics

(2010) Lars Konermann et al.   CHEMICAL SOCIETY REVIEWS

Stereo-specific synthesis of analogs of nerve agents and their utilization for selection and characterization of paraoxonase (PON1) catalytic scavengers

(2010) Y. Ashani et al.   CHEMICO-BIOLOGICAL INTERACTIONS

Computational Methods for De novo Protein Design and its Applications to the Human Immunodeficiency Virus 1, Purine Nucleoside Phosphorylase, Ubiquitin Specific Protease 7, and Histone Demethylases

(2010) M. Bellows et al.   CURRENT DRUG TARGETS

Biocatalysts by evolution

(2010) Christian Jäckel et al.   CURRENT OPINION IN BIOTECHNOLOGY

Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes

(2010) Bryan P Tracy et al.   CURRENT OPINION IN BIOTECHNOLOGY

Beyond directed evolution—semi-rational protein engineering and design

(2010) Stefan Lutz   CURRENT OPINION IN BIOTECHNOLOGY

Microfluidic droplets: new integrated workflows for biological experiments

(2010) Balint Kintses et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

What makes an enzyme promiscuous?

(2010) Ann Babtie et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Design strategies for the creation of artificial metalloenzymes

(2010) Tillmann Heinisch et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Ionic liquids in biotransformations: from proof-of-concept to emerging deep-eutectic-solvents

(2010) Pablo Domínguez de María et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst

(2010) Andreas S Bommarius et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Signatures of protein biophysics in coding sequence evolution

(2010) Claus O Wilke et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Flow cytometric sorting of the filamentous fungus Trichoderma reesei for improved strains

(2010) William Throndset et al.   ENZYME AND MICROBIAL TECHNOLOGY

Isolation of a strain of Trichoderma reesei with improved glucoamylase secretion by flow cytometric sorting

(2010) William Throndset et al.   ENZYME AND MICROBIAL TECHNOLOGY

IS LIFE IMPOSSIBLE? INFORMATION, SEX, AND THE ORIGIN OF COMPLEX ORGANISMS

(2010) Joel R. Peck et al.   EVOLUTION

Virtual screening with AutoDock: theory and practice

(2010) Sandro Cosconati et al.   Expert Opinion on Drug Discovery

Affibody molecules: Engineered proteins for therapeutic, diagnostic and biotechnological applications

(2010) J. Löfblom et al.   FEBS LETTERS

Enzyme-mediated oxidations for the chemist

(2010) Frank Hollmann et al.   GREEN CHEMISTRY

Improved precursor-directed biosynthesis in E. coli via directed evolution

(2010) Ho Young Lee et al.   JOURNAL OF ANTIBIOTICS

Evolution of Substrate Specificity within a Diverse Family of β/α-Barrel-fold Basic Amino Acid Decarboxylases

(2010) Xiaoyi Deng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A comparison of mass spectrometry based hydrogen deuterium exchange methods for probing the cyclophilin A cyclosporin complex

(2010) Stefan T. Esswein et al.   JOURNAL OF CHROMATOGRAPHY A

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein

(2010) Stefano Piana et al.   JOURNAL OF MOLECULAR BIOLOGY

Direct Analysis of Donor−Acceptor Distance and Relationship to Isotope Effects and the Force Constant for Barrier Compression in Enzymatic H-Tunneling Reactions

(2010) Christopher R. Pudney et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Manipulating the Stereoselectivity of Limonene Epoxide Hydrolase by Directed Evolution Based on Iterative Saturation Mutagenesis

(2010) Huabao Zheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Design and Elaboration of ade NovoHeterotetrameric α-Helical Protein That Selectively Binds an Emissive Abiological (Porphinato)zinc Chromophore

(2010) H. Christopher Fry et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Acyclic Chelate with Ideal Properties for68Ga PET Imaging Agent Elaboration

(2010) Eszter Boros et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Iterative Saturation Mutagenesis Accelerates Laboratory Evolution of Enzyme Stereoselectivity: Rigorous Comparison with Traditional Methods

(2010) Manfred T. Reetz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Controlling and Fine Tuning the Physical Properties of Two Identical Metal Coordination Sites in De Novo Designed Three Stranded Coiled Coil Peptides

(2010) Olga Iranzo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Intracellular ethanol accumulation in yeast cells during aerobic fermentation: a Raman spectroscopic exploration

(2010) L. Peng et al.   LETTERS IN APPLIED MICROBIOLOGY

Methods for detection and measurement of hydrogen peroxide inside and outside of cells

(2010) Sue Goo Rhee et al.   MOLECULES AND CELLS

Integrating carbon–halogen bond formation into medicinal plant metabolism

(2010) Weerawat Runguphan et al.   NATURE

Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome

(2010) Heinz Neumann et al.   NATURE

Predicting protein structures with a multiplayer online game

(2010) Seth Cooper et al.   NATURE

High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing

(2010) Mark Matzas et al.   NATURE BIOTECHNOLOGY

The role of physiological heterogeneity in microbial population behavior

(2010) Mary E Lidstrom et al.   Nature Chemical Biology

Rational assignment of key motifs for function guides in silico enzyme identification

(2010) Matthias Höhne et al.   Nature Chemical Biology

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Construction and testing of engineered zinc-finger proteins for sequence-specific modification of mtDNA

(2010) Michal Minczuk et al.   Nature Protocols

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

Where microbiology meets microengineering: design and applications of reporter bacteria

(2010) Jan Roelof van der Meer et al.   NATURE REVIEWS MICROBIOLOGY

ProteinDBS v2.0: a web server for global and local protein structure search

(2010) C.-R. Shyu et al.   NUCLEIC ACIDS RESEARCH

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides

(2010) Alex Y. Borovkov et al.   NUCLEIC ACIDS RESEARCH

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

(2010) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

(2010) Emily M. LeProust et al.   NUCLEIC ACIDS RESEARCH

RosettaBackrub--a web server for flexible backbone protein structure modeling and design

(2010) F. Lauck et al.   NUCLEIC ACIDS RESEARCH

Non-α-hydroxylated aldehydes with evolved transketolase enzymes

(2010) Armando Cázares et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

How an Enzyme Might Accelerate an Intramolecular Diels−Alder Reaction: Theozymes for the Formation of Salvileucalin B

(2010) Dean J. Tantillo   ORGANIC LETTERS

Evolutionary Innovations and the Organization of Protein Functions in Genotype Space

(2010) Evandro Ferrada et al.   PLoS One

Reengineering orthogonally selective riboswitches

(2010) N. Dixon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

(2010) M. P. Frushicheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

(2010) B. van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein interactions and ligand binding: From protein subfamilies to functional specificity

(2010) A. Rausell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrahigh-throughput screening in drop-based microfluidics for directed evolution

(2010) J. J. Agresti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination

(2010) Pete Heinzelman et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds

(2010) John Overington et al.   PROTEIN SCIENCE

Comparative characterization of random-sequence proteins consisting of 5, 12, and 20 kinds of amino acids

(2010) Junko Tanaka et al.   PROTEIN SCIENCE

Design principles for chlorophyll-binding sites in helical proteins

(2010) Paula Braun et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein rigidity and thermophilic adaptation

(2010) Sebastian Radestock et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The evolution and evolutionary consequences of marginal thermostability in proteins

(2010) Richard A. Goldstein   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE

Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture

(2010) C. K. Savile et al.   SCIENCE

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

(2010) J. B. Siegel et al.   SCIENCE

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

DREAMS of metabolism

(2010) Keng Cher Soh et al.   TRENDS IN BIOTECHNOLOGY

Event extraction for systems biology by text mining the literature

(2010) Sophia Ananiadou et al.   TRENDS IN BIOTECHNOLOGY

Circular permutation: a different way to engineer enzyme structure and function

(2010) Ying Yu et al.   TRENDS IN BIOTECHNOLOGY

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations

(2010) Raul Mendez et al.   PLoS Computational Biology

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

Gaussian process: an alternative approach for QSAM modeling of peptides

(2009) Peng Zhou et al.   AMINO ACIDS

Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment

(2009) Tiina S. Rasila et al.   ANALYTICAL BIOCHEMISTRY

H/D Exchange and Mass Spectrometry in the Studies of Protein Conformation and Dynamics: Is There a Need for a Top-Down Approach?

(2009) Igor A. Kaltashov et al.   ANALYTICAL CHEMISTRY

Controlling the Retention of Small Molecules in Emulsion Microdroplets for Use in Cell-Based Assays

(2009) Fabienne Courtois et al.   ANALYTICAL CHEMISTRY

Analysis of Protein Conformation and Dynamics by Hydrogen/Deuterium Exchange MS

(2009) John R. Engen   ANALYTICAL CHEMISTRY

Efficient Catalytic Promiscuity for Chemically Distinct Reactions

(2009) Ann C. Babtie et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structure-Guided Directed Evolution of Alkenyl and Arylmalonate Decarboxylases

(2009) Krzysztof Okrasa et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Engineering A Uranyl-Specific Binding Protein from NikR

(2009) Seraphine V. Wegner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Increased Malonyl Coenzyme A Biosynthesis by Tuning the Escherichia coli Metabolic Network and Its Application to Flavanone Production

(2009) Z. L. Fowler et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biosynthesis and biotechnological production of flavanones: current state and perspectives

(2009) Zachary L. Fowler et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Stability and solubility of proteins from extremophiles

(2009) Richard B. Greaves et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Application of flow cytometry to industrial microbial bioprocesses

(2009) Mario Díaz et al.   BIOCHEMICAL ENGINEERING JOURNAL

High-Resolution Crystal Structure of an Artificial (βα)8-Barrel Protein Designed from Identical Half-Barrels†‡

(2009) Birte Höcker et al.   BIOCHEMISTRY

Evolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms in Two Families ofcis,cis-Muconate Lactonizing Enzymes†‡

(2009) Ayano Sakai et al.   BIOCHEMISTRY

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

(2009) L. Xie et al.   BIOINFORMATICS

Genome-scale analysis of library sorting (GALibSo): Isolation of secretion enhancing factors for recombinant protein production inPichia pastoris

(2009) Gerhard Stadlmayr et al.   BIOTECHNOLOGY AND BIOENGINEERING

Biosynthesis of polylactic acid and its copolymers using evolved propionate CoA transferase and PHA synthase

(2009) Taek Ho Yang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Automated Alphabet Reduction for Protein Datasets

(2009) Jaume Bacardit et al.   BMC BIOINFORMATICS

SitesIdentify: a protein functional site prediction tool

(2009) Tracey Bray et al.   BMC BIOINFORMATICS

Massive non-natural proteins structure prediction using grid technologies

(2009) Giovanni Minervini et al.   BMC BIOINFORMATICS

An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

(2009) Huanting Liu et al.   BMC BIOTECHNOLOGY

MALS: an efficient strategy for multiple site-directed mutagenesis employing a combination of DNA amplification, ligation and suppression PCR

(2009) Alexey A Fushan et al.   BMC BIOTECHNOLOGY

Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases

(2009) Douglas B Kell   BMC Medical Genomics

Ultrahigh-Throughput FACS-Based Screening for Directed Enzyme Evolution

(2009) Guangyu Yang et al.   CHEMBIOCHEM

Engineering and improvement of the efficiency of a chimeric [P450cam-RhFRed reductase domain] enzyme

(2009) Aélig Robin et al.   CHEMICAL COMMUNICATIONS

In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature

(2009) Katarzyna Prymula et al.   CHEMISTRY & BIODIVERSITY

Expanding the Genetic Code for Biological Studies

(2009) Qian Wang et al.   CHEMISTRY & BIOLOGY

Searching NK Fitness Landscapes: On the Trade Off Between Speed and Quality in Complex Problem Solving

(2009) Sylvie Geisendorf   Computational Economics

Functional metagenomics for enzyme discovery: challenges to efficient screening

(2009) Taku Uchiyama et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational tools for designing and engineering biocatalysts

(2009) Jiri Damborsky et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Directed enzyme evolution: climbing fitness peaks one amino acid at a time

(2009) Cara A Tracewell et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Implications of the Dominant Role of Transporters in Drug Uptake by Cells (Supplementary Material)

(2009) Paul Dobson et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Harnessing natures ability to control metal ion coordination geometry using de novo designed peptides

(2009) Anna F. A. Peacock et al.   DALTON TRANSACTIONS

Science wikinomics. Mass networking through the web creates new forms of scientific collaboration

(2009) Andrea Rinaldi   EMBO REPORTS

Reinterpreting No Free Lunch

(2009) Jon E. Rowe et al.   EVOLUTIONARY COMPUTATION

Rational design of peptide-based building blocks for nanoscience and synthetic biology

(2009) Craig T. Armstrong et al.   FARADAY DISCUSSIONS

The Population Genetics of Adaptation: Multiple Substitutions on a Smooth Fitness Landscape

(2009) R. L. Unckless et al.   GENETICS

Closed-loop evolutionary multiobjective optimization

(2009) Joshua Knowles   IEEE Computational Intelligence Magazine

Glyphosate Resistance by Engineering the Flavoenzyme Glycine Oxidase

(2009) Mattia Pedotti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability

(2009) Pete Heinzelman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Exploring the Chemistry and Biology of Vanadium-dependent Haloperoxidases

(2009) Jaclyn M. Winter et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Flow cytometry-based method for isolating live bacteria with meta-cleavage activity on dihydroxy compounds of biphenyl

(2009) Sou Iijima et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Saturation-mutagenesis in two positions distant from active site of a Klebsiella pneumoniae glycerol dehydratase identifies some highly active mutants

(2009) Xianghui Qi et al.   JOURNAL OF BIOTECHNOLOGY

Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation

(2009) James Law et al.   Journal of Chemical Information and Modeling

Combinatorial design of protein sequences with applications to lattice and real proteins

(2009) Arnab Bhattacherjee et al.   JOURNAL OF CHEMICAL PHYSICS

Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins

(2009) Wei Zheng et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Global view of bionetwork dynamics: adaptive landscape

(2009) Ping Ao   Journal of Genetics and Genomics

Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series

(2009) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolving a Polymerase for Hydrophobic Base Analogues

(2009) David Loakes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Analysis of a complete DNA-protein affinity landscape

(2009) W. Rowe et al.   Journal of the Royal Society Interface

The Effect of Sequence Evolution on Protein Structural Divergence

(2009) Simon G. Williams et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expanded chemical diversity sampling through whole protein evolution

(2009) Amy J. Baldwin et al.   Molecular BioSystems

Advancing high-throughput gene synthesis technology

(2009) Jingdong Tian et al.   Molecular BioSystems

Moonlighting proteins—an update

(2009) Constance J. Jeffery   Molecular BioSystems

Design and engineering of an O2 transport protein

(2009) Ronald L. Koder et al.   NATURE

Mechanistic considerations of halogenating enzymes

(2009) Alison Butler et al.   NATURE

Design of functional metalloproteins

(2009) Yi Lu et al.   NATURE

Metalloproteins and metal sensing

(2009) Kevin J. Waldron et al.   NATURE

Protein promiscuity and its implications for biotechnology

(2009) Irene Nobeli et al.   NATURE BIOTECHNOLOGY

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

The far reaches of enzymology

(2009) Jesse G Zalatan et al.   Nature Chemical Biology

Enzymatic transition states and dynamic motion in barrier crossing

(2009) Steven D Schwartz et al.   Nature Chemical Biology

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Directed evolution drives the next generation of biocatalysts

(2009) Nicholas J Turner   Nature Chemical Biology

Fitness and its role in evolutionary genetics

(2009) H. Allen Orr   NATURE REVIEWS GENETICS

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Directed evolution of an orthogonal nucleoside analog kinase via fluorescence-activated cell sorting

(2009) Lingfeng Liu et al.   NUCLEIC ACIDS RESEARCH

HotSpot Wizard: a web server for identification of hot spots in protein engineering

(2009) A. Pavelka et al.   NUCLEIC ACIDS RESEARCH

The characterisation and catalytic properties of biomimetic metal–peptide complexes immobilised on mesoporous silica

(2009) Gerhard D. Pirngruber et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A Comprehensive Analysis of the Structure-Function Relationship in Proteins Based on Local Structure Similarity

(2009) Torgeir R. Hvidsten et al.   PLoS One

βα-Hairpin Clamps Brace βαβ Modules and Can Make Substantive Contributions to the Stability of TIM Barrel Proteins

(2009) Xiaoyan Yang et al.   PLoS One

Establishing wild-type levels of catalytic activity on natural and artificial (  )8-barrel protein scaffolds

(2009) J. Claren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzyme millisecond conformational dynamics do not catalyze the chemical step

(2009) A. V. Pisliakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A minimal sequence code for switching protein structure and function

(2009) Patrick A. Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A unified model of protein dynamics

(2009) H. Frauenfelder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

USER friendly DNA recombination (USERec): a simple and flexible near homology-independent method for gene library construction

(2009) B.R.M. Villiers et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Distributions of enzyme residues yielding mutants with improved substrate specificities from two different directed evolution strategies

(2009) J. Paramesvaran et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Evolutionary constraints on structural similarity in orthologs and paralogs

(2009) Mark E. Peterson et al.   PROTEIN SCIENCE

Cofactor binding and enzymatic activity in an unevolved superfamily ofde novodesigned 4-helix bundle proteins

(2009) Shona C. Patel et al.   PROTEIN SCIENCE

Circular permuted proteins in the universe of protein folds

(2009) Tobias Schmidt-Goenner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Automated scaffold selection for enzyme design

(2009) Christoph Malisi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Shape and evolution of thermostable protein structure

(2009) Ryan G. Coleman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Complete Reconstitution of a Highly Reducing Iterative Polyketide Synthase

(2009) S. M. Ma et al.   SCIENCE

The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

(2009) Alison Cuff et al.   STRUCTURE

Catalytic effectiveness, a measure of enzyme proficiency for industrial applications

(2009) Richard J. Fox et al.   TRENDS IN BIOTECHNOLOGY

An automatic method for assessing structural importance of amino acid positions

(2009) Michael I Sadowski et al.   BMC STRUCTURAL BIOLOGY

A generic method for assignment of reliability scores applied to solvent accessibility predictions

(2009) Bent Petersen et al.   BMC STRUCTURAL BIOLOGY

Recombinational Landscape and Population Genomics of Caenorhabditis elegans

(2009) Matthew V. Rockman et al.   PLoS Genetics

Peptide and Protein Building Blocks for Synthetic Biology: From Programming Biomolecules to Self-Organized Biomolecular Systems

(2008) Elizabeth H. C. Bromley et al.   ACS Chemical Biology

Single-Cell High-Throughput Screening To Identify Enantioselective Hydrolytic Enzymes

(2008) Stefan Becker et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Artificial Enzymes Made to Order: Combination of Computational Design and Directed Evolution

(2008) Thomas R. Ward   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protein Design by Directed Evolution

(2008) Christian Jäckel et al.   Annual Review of Biophysics

Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates

(2008) Joaquin Sanchis et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Directed evolution of aldolases for exploitation in synthetic organic chemistry

(2008) Amanda Bolt et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Controlling complexity and water penetration in functionalde novoprotein design

(2008) J.L. Ross Anderson et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Free-Energy Landscape of Enzyme Catalysis†

(2008) Stephen J. Benkovic et al.   BIOCHEMISTRY

Incorporation of Hydrostatic Pressure into Models of Hydrogen Tunneling Highlights a Role for Pressure-Modulated Promoting Vibrations†

(2008) Sam Hay et al.   BIOCHEMISTRY

Descriptor-free molecular discovery in large libraries by adaptive substituent reordering

(2008) Scott R. McAllister et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

(2008) Jonathan G Lees et al.   BMC BIOINFORMATICS

A Novel Genetic Selection System for Improved Enantioselectivity ofBacillus subtilis Lipase A

(2008) Ykelien L. Boersma et al.   CHEMBIOCHEM

Addressing the Numbers Problem in Directed Evolution

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM

A genetic selection system for evolving enantioselectivity of enzymes

(2008) Manfred T. Reetz et al.   CHEMICAL COMMUNICATIONS

In Vitro Reconstituted Biotransformation of 4-Fluorothreonine from Fluoride Ion: Application of the Fluorinase

(2008) Hai Deng et al.   CHEMISTRY & BIOLOGY

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

The fluorinase, the chlorinase and the duf-62 enzymes

(2008) Hai Deng et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Zn(ii), Cd(ii) and Pb(ii) complexation with pyridinecarboxylate containing ligands

(2008) Raquel Ferreirós-Martínez et al.   DALTON TRANSACTIONS

‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries

(2008) Paul D. Dobson et al.   DRUG DISCOVERY TODAY

Creating protein biocatalysts as tools for future industrial applications

(2008) John C Chaput et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Alternative binding proteins: Anticalins - harnessing the structural plasticity of the lipocalin ligand pocket to engineer novel binding activities

(2008) Arne Skerra   FEBS Journal

Alternative binding proteins: Affibody binding proteins developed from a small three-helix bundle scaffold

(2008) Per-Åke Nygren   FEBS Journal

Biocatalysis for the Production of Industrial Products and Functional Foods from Rice and Other Agricultural Produce

(2008) Casimir C. Akoh et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

A modified method for PCR-directed gene synthesis from large number of overlapping oligodeoxyribonucleotides

(2008) Jessica Cherry et al.  

Changes of Protein Folding Pathways by Circular Permutation

(2008) Ellinor Haglund et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metal ions in biological catalysis: from enzyme databases to general principles

(2008) Claudia Andreini et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Directed evolution of transketolase substrate specificity towards an aliphatic aldehyde

(2008) E HIBBERT et al.   JOURNAL OF BIOTECHNOLOGY

Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space

(2008) Helena Strömbergsson et al.   Journal of Chemical Information and Modeling

Structure−Activity Landscape Index:  Identifying and Quantifying Activity Cliffs

(2008) Rajarshi Guha et al.   Journal of Chemical Information and Modeling

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness

(2008) Josselin Noirel et al.   JOURNAL OF CHEMICAL PHYSICS

Assessment of programs for ligand binding affinity prediction

(2008) Ryangguk Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Evolutionary History of a Specialized P450 Propane Monooxygenase

(2008) Rudi Fasan et al.   JOURNAL OF MOLECULAR BIOLOGY

The Structure of Monoamine Oxidase from Aspergillus niger Provides a Molecular Context for Improvements in Activity Obtained by Directed Evolution

(2008) Kate E. Atkin et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantum Mechanical Design of Enzyme Active Sites

(2008) Xiyun Zhang et al.   JOURNAL OF ORGANIC CHEMISTRY

The Complex Inter-Relationships Between Protein Flexibility and Stability

(2008) Tim J. Kamerzell et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Mouse Organic Anion Transporter 2 (mOat2) Mediates the Transport of Short Chain Fatty Acid Propionate

(2008) Rafiqul Islam et al.   JOURNAL OF PHARMACOLOGICAL SCIENCES

Efficient Catalytic Promiscuity in an Enzyme Superfamily: An Arylsulfatase Shows a Rate Acceleration of 1013for Phosphate Monoester Hydrolysis

(2008) Luis F. Olguin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-Throughput Selection for Cellulase Catalysts Using Chemical Complementation

(2008) Pamela Peralta-Yahya et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Metal−Peptide Frameworks (MPFs):  “Bioinspired” Metal Organic Frameworks

(2008) Alexandre Mantion et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Designed α-Helical Tectons for Constructing Multicomponent Synthetic Biological Systems

(2008) Elizabeth H. C. Bromley et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hierarchical distribution of ascending slopes, nearly neutral networks, highlands, and local optima at the dth order in an NK fitness landscape

(2008) Takuyo Aita   JOURNAL OF THEORETICAL BIOLOGY

Fitting protein-folding free energy landscape for a certain conformation to an NK fitness landscape

(2008) Takuyo Aita et al.   JOURNAL OF THEORETICAL BIOLOGY

In silico modelling of directed evolution: Implications for experimental design and stepwise evolution

(2008) David C. Wedge et al.   JOURNAL OF THEORETICAL BIOLOGY

Exploiting genetic diversity by directed evolution: molecular breeding of type III polyketide synthases improves productivity

(2008) Wenjuan Zha et al.   Molecular BioSystems

Shedding light on the efficacy of laboratory evolution based on iterative saturation mutagenesis

(2008) Manfred T. Reetz et al.   Molecular BioSystems

Strain Improvement of RecombinantEscherichia colifor Efficient Production of Plant Flavonoids

(2008) Effendi Leonard et al.   MOLECULAR PHARMACEUTICS

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

(2008) Lukas Burger et al.   Molecular Systems Biology

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Highly active and selective endopeptidases with programmed substrate specificities

(2008) Navin Varadarajan et al.   Nature Chemical Biology

Directed enzyme evolution via small and effective neutral drift libraries

(2008) Rinkoo D Gupta et al.   NATURE METHODS

Substrate-induced gene expression (SIGEX) screening of metagenome libraries

(2008) Taku Uchiyama et al.   Nature Protocols

Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule?

(2008) Paul D. Dobson et al.   NATURE REVIEWS DRUG DISCOVERY

Neutralism and selectionism: a network-based reconciliation

(2008) Andreas Wagner   NATURE REVIEWS GENETICS

Cell-free protein synthesis: applications in proteomics and biotechnology

(2008) Mingyue He   New Biotechnology

Linking the functions of unrelated proteins using a novel directed evolution domain insertion method

(2008) Wayne R. Edwards et al.   NUCLEIC ACIDS RESEARCH

Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

(2008) Christopher G. Knight et al.   NUCLEIC ACIDS RESEARCH

GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries

(2008) A. E. Firth et al.   NUCLEIC ACIDS RESEARCH

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

(2008) Zengyi Shao et al.   NUCLEIC ACIDS RESEARCH

Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx)

(2008) Amy J. Baldwin et al.   NUCLEIC ACIDS RESEARCH

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies

(2008) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

Solvent viscosity dependence for enzymatic reactions

(2008) A.E. Sitnitsky   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions

(2008) R. K. Eppler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein evolution with an expanded genetic code

(2008) C. C. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome

(2008) D. G. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility

(2008) P. E. Tomatis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bioinformatic method for protein thermal stabilization by structural entropy optimization

(2008) E. Bae et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A   -barrel built by the combination of fragments from different folds

(2008) T. A. M. Bharat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution

(2008) Aurelio Hidalgo et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Amino acid alphabet size in protein evolution experiments: better to search a small library thoroughly or a large library sparsely?

(2008) E. Munoz et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Structure-based protein engineering efforts with a monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties

(2008) M. Alahuhta et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Thermostable variants constructed via the structure-guided consensus method also show increased stability in salts solutions and homogeneous aqueous-organic media

(2008) E. Vazquez-Figueroa et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Deriving protein dynamical properties from weighted protein contact number

(2008) Chih-Peng Lin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains

(2008) Catherine L. Worth et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

(2008) D. G. Gibson et al.   SCIENCE

Enzyme optimization: moving from blind evolution to statistical exploration of sequence–function space

(2008) Richard J. Fox et al.   TRENDS IN BIOTECHNOLOGY

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology

A microplate-based evaluation of complex denaturation pathways: Structural stability ofEscherichia coli transketolase

(2007) Jean P. Aucamp et al.   BIOTECHNOLOGY AND BIOENGINEERING

Transversion-enriched sequence saturation mutagenesis (SeSaM-Tv+): A random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error-prone PCR

(2007) Tuck Seng Wong et al.   Biotechnology Journal

Computationally Mapping Sequence Space To Understand Evolutionary Protein Engineering

(2007) K.A. Armstrong et al.   BIOTECHNOLOGY PROGRESS

Synthesis of chiral pharmaceutical intermediates by biocatalysis

(2007) Ramesh N. Patel   COORDINATION CHEMISTRY REVIEWS

Detecting LTR structures in human genomic sequences using profile hidden Markov models

(2007) Li-Ching Wu et al.   EXPERT SYSTEMS WITH APPLICATIONS

Selecting Folded Proteins from a Library of Secondary Structural Elements

(2007) James J. Graziano et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Construction and characterization of protein libraries composed of secondary structure modules

(2002) Tomoaki Matsuura et al.   PROTEIN SCIENCE