Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation

Predictive Bcl-2 Family Binding Models Rooted in Experiment or Structure

(2012) Joe DeBartolo et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design

(2012) Elisabeth Humphris-Narayanan et al.   PLoS Computational Biology

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

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

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

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

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

Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface

(2011) Mariana Babor et al.   PROTEIN SCIENCE

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity

(2011) Nir London et al.   PLoS Computational Biology

Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library

(2010) Shaun M. Lippow et al.   CHEMISTRY & BIOLOGY

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

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

Identifying and Seeing beyond Multiple Sequence Alignment Errors Using Intra-Molecular Protein Covariation

(2010) Russell J. Dickson et al.   PLoS One

Structure-based prediction of protein-peptide specificity in rosetta

(2010) Christopher A. King et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2009) Daniel J Mandell et al.   NATURE METHODS

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

(2009) Gregory D. Friedland et al.   PLoS Computational Biology

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

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

Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design

(2008) Elisabeth L. Humphris et al.   STRUCTURE

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology

Thoroughly sampling sequence space: Large-scale protein design of structural ensembles

(2002) Stefan M. Larson et al.   PROTEIN SCIENCE