Physics-based enzyme design: Predicting binding affinity and catalytic activity

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

Computational Enzyme Design

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

De novo enzymes by computational design

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

Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking

(2013) G. Madhavi Sastry et al.   Journal of Chemical Information and Modeling

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

(2013) Lingle Wang et al.   Journal of Chemical Theory and Computation

Computational design of ligand-binding proteins with high affinity and selectivity

(2013) Christine E. Tinberg et al.   NATURE

Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes

(2013) Hege Beard et al.   PLoS One

Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering

(2012) David J. Osguthorpe et al.   Chemical Biology & Drug Design

Emerging themes in the computational design of novel enzymes and protein-protein interfaces

(2012) Sagar D. Khare et al.   FEBS LETTERS

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

Computational Design of an α-Gliadin Peptidase

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

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

Redesigning and characterizing the substrate specificity and activity of Vibrio fluvialis aminotransferase for the synthesis of imagabalin

(2012) K. S. Midelfort et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Contribution of Explicit Solvent Effects to the Binding Affinity of Small-Molecule Inhibitors in Blood Coagulation Factor Serine Proteases

(2011) Robert Abel et al.   ChemMedChem

Designing a New Diels–Alderase: A Combinatorial, Semirational Approach Including Dynamic Optimization.

(2011) Mats Linder et al.   Journal of Chemical Information and Modeling

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling

(2011) Jianing Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Antibody modeling assessment

(2011) Juan C. Almagro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

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

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

(2010) J. B. Siegel et al.   SCIENCE

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

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

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