Predicting enzymatic reactivity: from theory to design

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

De novo enzymes by computational design

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

QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis

(2013) Marc W. van der Kamp et al.   FEBS Journal

Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies

(2013) Kirill Zinovjev et al.   Journal of Chemical Theory and Computation

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

(2013) Rafael García-Meseguer et al.   Nature Chemistry

A Collective Coordinate to Obtain Free Energy Profiles for Complex Reactions in Condensed Phases

(2012) Kirill Zinovjev et al.   Journal of Chemical Theory and Computation

Computational Design of an α-Gliadin Peptidase

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

Crucial Role of Protein Flexibility in Formation of a Stable Reaction Transition State in an α-Amylase Catalysis

(2012) Takahiro Kosugi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Good vibrations in enzyme-catalysed reactions

(2012) Sam Hay et al.   Nature Chemistry

Taking Ockham's razor to enzyme dynamics and catalysis

(2012) David R. Glowacki et al.   Nature Chemistry

Theoretical studies of HIV-1 reverse transcriptase inhibition

(2012) Katarzyna Świderek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase

(2012) A. T. Fafarman 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

Robust design and optimization of retroaldol enzymes

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

Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis

(2011) Gordon G. Hammes et al.   BIOCHEMISTRY

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

(2011) Victor Ovchinnikov et al.   JOURNAL OF CHEMICAL PHYSICS

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

(2011) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase

(2011) S. K. Jha 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

Dynamics and dissipation in enzyme catalysis

(2011) N. Boekelheide et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The quantum chemical cluster approach for modeling enzyme reactions

(2011) Per E.M. Siegbahn et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Hibernating Bears, Antibiotics, and the Evolving Ribosome (Nobel Lecture)

(2010) Ada Yonath   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Coupled motions in enzyme catalysis

(2010) Vishal C Nashine 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

Importance of the Lactate Dehydrogenase Quaternary Structure in Theoretical Calculations

(2010) Katarzyna Świderek et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Testing High-Level QM/MM Methods for Modeling Enzyme Reactions: Acetyl-CoA Deprotonation in Citrate Synthase

(2010) Marc W. van der Kamp et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Editing Mechanism of Aminoacyl-tRNA Synthetases Operates by a Hybrid Ribozyme/Protein Catalyst

(2010) Yohsuke Hagiwara et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

(2010) J. B. Siegel et al.   SCIENCE

Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

(2009) Dhruva K. Chakravorty et al.   BIOCHEMISTRY

Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H

(2009) Edina Rosta et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Design of functional metalloproteins

(2009) Yi Lu et al.   NATURE

Designing artificial enzymes by intuition and computation

(2009) Vikas Nanda et al.   Nature Chemistry

Computational structure-based redesign of enzyme activity

(2009) C.-Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alteration of enzyme specificity by computational loop remodeling and design

(2009) P. M. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate

(2008) Anna L. Bowman et al.   CHEMICAL COMMUNICATIONS

Computational design of biological catalysts

(2008) Sergio Martí et al.   CHEMICAL SOCIETY REVIEWS

Predicting an Improvement of Secondary Catalytic Activity of Promiscuos Isochorismate Pyruvate Lyase by Computational Design

(2008) Sergio Martí et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach

(2008) J. Javier Ruiz-Pernía 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