CADEE: Computer-Aided Directed Evolution of Enzymes

Catalytic Promiscuity of Transaminases: Preparation of Enantioenriched β-Fluoroamines by Formal Tandem Hydrodefluorination/Deamination

(2016) Aníbal Cuetos et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase

(2016) Geir Villy Isaksen et al.   BIOCHEMISTRY

Structure–Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase

(2016) John P. Richard et al.   BIOCHEMISTRY

HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering

(2016) Jaroslav Bendl et al.   NUCLEIC ACIDS RESEARCH

Conformational diversity and enantioconvergence in potato epoxide hydrolase 1

(2016) P. Bauer et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Molecular Dynamics Explorations of Active Site Structure in Designed and Evolved Enzymes

(2015) Sílvia Osuna et al.   ACCOUNTS OF CHEMICAL RESEARCH

Enantioselective Enzymes by Computational Design and In Silico Screening

(2015) Hein J. Wijma et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Computational strategies for the design of new enzymatic functions

(2015) K. Świderek et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Production of biofuels and biochemicals by in vitro synthetic biosystems: Opportunities and challenges

(2015) Yi-Heng Percival Zhang   BIOTECHNOLOGY ADVANCES

Industrial applications of enzyme biocatalysis: Current status and future aspects

(2015) Jung-Min Choi et al.   BIOTECHNOLOGY ADVANCES

Recent developments in biocatalysis beyond the laboratory

(2015) Tanja Narancic et al.   BIOTECHNOLOGY LETTERS

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

(2015) Andrew Currin et al.   CHEMICAL SOCIETY REVIEWS

High-Level QM/MM Calculations Support the Concerted Mechanism for Michael Addition and Covalent Complex Formation in Thymidylate Synthase

(2015) Nopporn Kaiyawet et al.   Journal of Chemical Theory and Computation

Catalytic Stimulation by Restrained Active-Site Floppiness—The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1

(2015) Moshe Ben-David et al.   JOURNAL OF MOLECULAR BIOLOGY

Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems

(2015) Geir Villy Isaksen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase

(2015) Xiang Zhai et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily

(2015) Alexandre Barrozo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Methods for the directed evolution of proteins

(2015) Michael S. Packer et al.   NATURE REVIEWS GENETICS

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization

(2015) Jeronimo Lameira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biocatalysis: A Status Report

(2015) Andreas S. Bommarius   Annual Review of Chemical and Biomolecular Engineering

Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

(2015) Katarzyna Świderek et al.   ACS Catalysis

Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes

(2015) Beat A. Amrein et al.   ACS Catalysis

New Generation of Biocatalysts for Organic Synthesis

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

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

Computer aided enzyme design and catalytic concepts

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

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

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

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

(2014) Vojtěch Mlýnský et al.   Journal of Chemical Theory and Computation

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

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

Density functional tight binding: values of semi-empirical methods in an ab initio era

(2014) Qiang Cui et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case

(2013) Maria E. S. Lind et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Inversion of Enantioselectivity of a Mononuclear Non-Heme Iron(II)-dependent Hydroxylase by Tuning the Interplay of Metal-Center Geometry and Protein Structure

(2013) Sarah M. Pratter et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Computational Enzyme Design

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

Structural Mutations That Probe the Interactions between the Catalytic and Dianion Activation Sites of Triosephosphate Isomerase

(2013) Xiang Zhai et al.   BIOCHEMISTRY

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

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

De novo enzymes by computational design

(2013) Hajo Kries 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

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

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

Advances in the Process Development of Biocatalytic Processes

(2013) Pär Tufvesson et al.   ORGANIC PROCESS RESEARCH & DEVELOPMENT

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

Semiempirical quantum-chemical methods

(2013) Walter Thiel   Wiley Interdisciplinary Reviews-Computational Molecular Science

A Paradigm for Enzyme-Catalyzed Proton Transfer at Carbon: Triosephosphate Isomerase

(2012) John P. Richard   BIOCHEMISTRY

Many Pathways in Laboratory Evolution Can Lead to Improved Enzymes: How to Escape from Local Minima

(2012) Yosephine Gumulya et al.   CHEMBIOCHEM

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

(2012) Jinghui Luo et al.   FEBS LETTERS

Engineering the third wave of biocatalysis

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

A Computational Methodology to Screen Activities of Enzyme Variants

(2012) Martin R. Hediger et al.   PLoS One

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

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

COMPUTATIONAL APPROACHES FOR RATIONAL DESIGN OF PROTEINS WITH NOVEL FUNCTIONALITIES

(2012) Manish Kumar Tiwari 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

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

(2011) Maria P. Frushicheva et al.   BIOCHEMISTRY

Mechanism for Activation of Triosephosphate Isomerase by Phosphite Dianion: The Role of a Ligand-Driven Conformational Change

(2011) M. Merced Malabanan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The empirical valence bond model: theory and applications

(2011) Shina C. L. Kamerlin et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Triosephosphate isomerase: a highly evolved biocatalyst

(2010) R. K. Wierenga et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

(2010) S. C. L. Kamerlin 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

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

(2010) C. K. Savile et al.   SCIENCE

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Toward Accurate Screening in Computer-Aided Enzyme Design†

(2009) Maite Roca et al.   BIOCHEMISTRY

The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

(2009) Shina C. L. Kamerlin et al.   FARADAY DISCUSSIONS

Exploring protein fitness landscapes by directed evolution

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

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Design by Directed Evolution

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

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE