Computational Enzyme Design

Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis

(2012) Florian Richter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient, Chemoenzymatic Process for Manufacture of the Boceprevir Bicyclic [3.1.0]Proline Intermediate Based on Amine Oxidase-Catalyzed Desymmetrization

(2012) Tao Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineering the third wave of biocatalysis

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

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

(2012) Christopher B Eiben et al.   NATURE BIOTECHNOLOGY

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

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

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

Discovery and Protein Engineering of Biocatalysts for Organic Synthesis

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

Design of a Three-Helix Bundle Capable of Binding Heavy Metals in a Triscysteine Environment

(2011) Saumen Chakraborty et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2011) Maria P. Frushicheva et al.   BIOCHEMISTRY

Enhanced Expression and Purification of Fungal Galactose Oxidase in Escherichia coli and Use for Analysis of a Saturation Mutagenesis Library

(2011) Sarah E. Deacon  et al.   CHEMBIOCHEM

Application of Designed Enzymes in Organic Synthesis

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

New opportunities for biocatalysis: driving the synthesis of chiral chemicals

(2011) Gao-Wei Zheng et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Catalytic Proficiency: The Extreme Case of S–O Cleaving Sulfatases

(2011) David R. Edwards et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Design of a β-Peptide That Targets Transmembrane Helices

(2011) Scott J. Shandler et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A De Novo Protein Binding Pair By Computational Design and Directed Evolution

(2011) John Karanicolas et al.   MOLECULAR CELL

The next step for the synthetic genome

(2011) Monya Baker   NATURE

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9

(2011) Jason S. McLellan et al.   NATURE

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

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

Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering

(2011) Umut Y. Ulge et al.   NUCLEIC ACIDS RESEARCH

Nerve Agent Hydrolysis Activity Designed into a Human Drug Metabolism Enzyme

(2011) Andrew C. Hemmert et al.   PLoS One

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

Algorithm discovery by protein folding game players

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

Design of a switchable eliminase

(2011) I. V. Korendovych et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational design of an endo-1,4- -xylanase ligand binding site

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

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

(2011) G. Grigoryan et al.   SCIENCE

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

(2011) X. Wu et al.   SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

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

Genome mining approach for the discovery of novel cytochrome P450 biocatalysts

(2010) Toshiki Furuya et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Optimizing non-natural protein function with directed evolution

(2010) Eric M Brustad 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

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

Predicting protein structures with a multiplayer online game

(2010) Seth Cooper et al.   NATURE

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

(2010) Justin Ashworth et al.   NUCLEIC ACIDS RESEARCH

Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole

(2010) D. A. Kraut 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

Origins of catalysis by computationally designed retroaldolase enzymes

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

Evaluation and ranking of enzyme designs

(2010) Gert Kiss et al.   PROTEIN 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

Creation of an Amino Acid Network of Structurally Coupled Residues in the Directed Evolution of a Thermostable Enzyme

(2009) Manfred T. Reetz et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enzyme (re)design: lessons from natural evolution and computation

(2009) John A Gerlt et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

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

The Influence of Protein Dynamics on the Success of Computational Enzyme Design

(2009) Jory Z. Ruscio et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity

(2009) Jean-Christophe Baret et al.   LAB ON A CHIP

Advancing high-throughput gene synthesis technology

(2009) Jingdong Tian et al.   Molecular BioSystems

Exploitation of binding energy for catalysis and design

(2009) Summer B. Thyme et al.   NATURE

The changing economics of DNA synthesis

(2009) Robert Carlson   NATURE BIOTECHNOLOGY

Designing artificial enzymes by intuition and computation

(2009) Vikas Nanda et al.   Nature Chemistry

An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket

(2009) E. W. Debler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational design of ligand binding is not a solved problem

(2009) B. Schreier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete Inversion of Enantioselectivity towards Acetylated Tertiary Alcohols by a Double Mutant of aBacillus Subtilis Esterase

(2008) Sebastian Bartsch et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protein Design by Directed Evolution

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

Mechanisms and structures of crotonase superfamily enzymes – How nature controls enolate and oxyanion reactivity

(2008) R. B. Hamed et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Catalytic Activity of Certain Antibodies as a Potential Tool for Drug Synthesis and for Directed Prodrug Therapies

(2008) T. Wojcik et al.   CURRENT MEDICINAL CHEMISTRY

Advances in laboratory evolution of enzymes

(2008) Shimon Bershtein et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Design of Protein–Ligand Binding Based on the Molecular-Mechanics Energy Model

(2008) F. Edward Boas et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Reorganization and Preorganization in Enzyme Active Sites: Comparisons of Experimental and Theoretically Ideal Active Site Geometries in the Multistep Serine Esterase Reaction Cycle

(2008) Adam J. T. Smith et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination

(2008) Anastassia N. Alexandrova et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE