Predicting Evolutionary Site Variability from Structure in Viral Proteins: Buriedness, Packing, Flexibility, and Design

CircStat: AMATLABToolbox for Circular Statistics

(2015) Philipp Berens   Journal of Statistical Software

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility

(2014) Tsun-Tsao Huang et al.   BMC EVOLUTIONARY BIOLOGY

Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure

(2013) Joseph A. Marsh et al.   BIOESSAYS

Structural dynamics flexibility informs function and evolution at a proteome scale

(2013) Zeynep Nevin Gerek et al.   Evolutionary Applications

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Membrane Environment Imposes Unique Selection Pressures on Transmembrane Domains of G Protein-Coupled Receptors

(2013) Stephanie J. Spielman et al.   JOURNAL OF MOLECULAR EVOLUTION

A New Formulation of Protein Evolutionary Models that Account for Structural Constraints

(2013) Andrew J. Bordner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure

(2013) So-Wei Yeh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Amino-acid site variability among natural and designed proteins

(2013) Eleisha L. Jackson et al.   PeerJ

Modeling coding-sequence evolution within the context of residue solvent accessibility

(2012) Michael P Scherrer et al.   BMC EVOLUTIONARY BIOLOGY

Integrating Sequence Variation and Protein Structure to Identify Sites under Selection

(2012) Austin G. Meyer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence Evolution Correlates with Structural Dynamics

(2012) Ying Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

Evolutionary information hidden in a single protein structure

(2012) Chien-Hua Shih et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution

(2011) Duncan C. Ramsey et al.   GENETICS

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

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

Signatures of protein biophysics in coding sequence evolution

(2010) Claus O Wilke et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds

(2010) John Overington et al.   PROTEIN SCIENCE

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Structural Determinants of Protein Evolution Are Context-Sensitive at the Residue Level

(2009) E. A. Franzosa et al.   MOLECULAR BIOLOGY AND EVOLUTION

A perturbative view of protein structural variation

(2009) Julián Echave et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evolutionary conservation of protein vibrational dynamics

(2008) Sandra Maguid et al.   GENE

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

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE