The utility of protein structure as a predictor of site-wise dN/dSvaries widely among HIV-1 proteins

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

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

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

Structure and immune recognition of trimeric pre-fusion HIV-1 Env

(2014) Marie Pancera et al.   NATURE

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

(2013) Carina F. Mugal 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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

(2013) A. G. Meyer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Maximum Allowed Solvent Accessibilites of Residues in Proteins

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

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

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

Bringing Molecules Back into Molecular Evolution

(2012) Claus O. Wilke   PLoS Computational Biology

Biophysical and structural considerations for protein sequence evolution

(2011) Johan A Grahnen et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Duncan C. Ramsey et al.   GENETICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

X-Ray Structures of the Hexameric Building Block of the HIV Capsid

(2009) Owen Pornillos 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

Do viral proteins possess unique biophysical features?

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

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics