Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

(2014) C. Melero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Motif-directed redesign of enzyme specificity

(2014) Benjamin Borgo et al.   PROTEIN SCIENCE

Evolution of oligomeric state through allosteric pathways that mimic ligand binding

(2014) Tina Perica et al.   SCIENCE

Computational design of protein-small molecule interfaces

(2013) Brittany Allison et al.   JOURNAL OF STRUCTURAL BIOLOGY

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

PDBe: Protein Data Bank in Europe

(2013) Aleksandras Gutmanas et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation

(2013) Noah Ollikainen et al.   PLoS Computational Biology

Directed enzyme evolution: beyond the low-hanging fruit

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

Binding Pocket Optimization by Computational Protein Design

(2012) Christoph Malisi et al.   PLoS One

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

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

The Role of Local Backrub Motions in Evolved and Designed Mutations

(2012) Daniel A. Keedy et al.   PLoS Computational Biology

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

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

Accessing protein conformational ensembles using room-temperature X-ray crystallography

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

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors

(2010) Antonija Kuzmanic et al.   BIOPHYSICAL JOURNAL

Optimizing non-natural protein function with directed evolution

(2010) Eric M Brustad et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains

(2010) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

Manufacturing Molecules Through Metabolic Engineering

(2010) J. D. Keasling   SCIENCE

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

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

Computational design of second-site suppressor mutations at protein-protein interfaces

(2009) Deanne W. Sammond et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY