Causes of evolutionary rate variation among protein sites

Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs

(2015) Michael B. Doud et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Relationship between dN/dS and Scaled Selection Coefficients

(2015) Stephanie J. Spielman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Probabilistic models of eukaryotic evolution: time for integration

(2015) Nicolas Lartillot   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme

(2015) Luciano A. Abriata et al.   PLoS One

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein

(2015) Yu-Wen Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Systematic humanization of yeast genes reveals conserved functions and genetic modularity

(2015) A. H. Kachroo et al.   SCIENCE

Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin

(2015) Austin G. Meyer et al.   PLoS Pathogens

Too packed to change: side-chain packing and site-specific substitution rates in protein evolution

(2015) María Laura Marcos et al.   PeerJ

FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures

(2014) Yi-Fei Huang et al.   BIOINFORMATICS

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

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

(2014) Amir Shahmoradi et al.   JOURNAL OF MOLECULAR EVOLUTION

An Experimentally Informed Evolutionary Model Improves Phylogenetic Fit to Divergent Lactamase Homologs

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Estimation of Nonsynonymous/Synonymous Rate Ratios for Pairwise Sequence Comparisons

(2014) K. Angelis et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

(2014) Ryan R. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase

(2014) Nicole G. H. Leferink et al.   Nature Communications

Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures

(2014) Yi-Fei Huang et al.   PLoS Computational 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

Quantitative Residue-Level Structure–Evolution Relationships in the Yeast Membrane Proteome

(2013) Eric A. Franzosa et al.   Genome Biology and Evolution

On the Need for Mechanistic Models in Computational Genomics and Metagenomics

(2013) David A. Liberles et al.   Genome Biology and Evolution

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

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

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell 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

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation

(2013) Noah Ollikainen et al.   PLoS Computational Biology

Amino-acid site variability among natural and designed proteins

(2013) Eleisha L. Jackson et al.   PeerJ

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

(2012) Philippe Lemey et al.   BIOINFORMATICS

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

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

On the Statistical Interpretation of Site-Specific Variables in Phylogeny-Based Substitution Models

(2012) N. Rodrigue   GENETICS

Integrating Sequence Variation and Protein Structure to Identify Sites under Selection

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

Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection

(2012) C. Tusche et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence Evolution Correlates with Structural Dynamics

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

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Independent Effects of Protein Core Size and Expression on Residue-Level Structure-Evolution Relationships

(2012) Eric A. Franzosa et al.   PLoS One

Amino acid coevolution induces an evolutionary Stokes shift

(2012) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

(2012) J.-R. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Rational Engineering of Enzyme Allosteric Regulation through Sequence Evolution Analysis

(2012) Jae-Seong Yang et al.   PLoS Computational Biology

Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation

(2012) C. Scott Wylie et al.   PLoS Computational Biology

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

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

(2011) Duncan C. Ramsey et al.   GENETICS

Quantifying selection and diversity in viruses by entropy methods, with application to the haemagglutinin of H3N2 influenza

(2011) K. Pan et al.   Journal of the Royal Society Interface

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

Slow protein evolutionary rates are dictated by surface-core association

(2011) A. Toth-Petroczy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A biophysical protein folding model accounts for most mutational fitness effects in viruses

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

Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins

(2011) Sergey Kryazhimskiy et al.   PLoS Genetics

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

A comparative study of conservation and variation scores

(2010) Fredrik Johansson et al.   BMC BIOINFORMATICS

Statistical Potentials for Improved Structurally Constrained Evolutionary Models

(2010) Claudia L. Kleinman et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Benchmarking Multi-Rate Codon Models

(2010) Wayne Delport et al.   PLoS One

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Solvent Accessible Surface Area of Amino Acid Residues in Globular Proteins: Correlation of Apparent Transfer Free Energies with Experimental Hydrophobicity Scales

(2009) Alexey K. Shaytan et al.   BIOMACROMOLECULES

Solvent Exposure Imparts Similar Selective Pressures across a Range of Yeast Proteins

(2009) G. C. Conant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparing Models of Evolution for Ordered and Disordered Proteins

(2009) C. J. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Protein elastic network models and the ranges of cooperativity

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin

(2009) Jesse D. Bloom et al.   PLoS Computational Biology

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative

(2008) Andrew D. Fernandes et al.   BIOINFORMATICS

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

(2008) Huai-Chun Wang et al.   BMC EVOLUTIONARY BIOLOGY

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

Contact Density Affects Protein Evolutionary Rate from Bacteria to Animals

(2008) Tong Zhou et al.   JOURNAL OF MOLECULAR EVOLUTION

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

(2008) M. T Holder et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Deriving protein dynamical properties from weighted protein contact number

(2008) Chih-Peng Lin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Do viral proteins possess unique biophysical features?

(2008) Nobuhiko Tokuriki et al.   TRENDS IN BIOCHEMICAL SCIENCES

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

(2008) Jonathan M. Carlson et al.   PLoS Computational Biology