Selection on protein structure, interaction, and sequence

Positive Selection Analysis of Overlapping Reading Frames Is Invalid

(2015) Christopher Monit et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Conformational diversity and the emergence of sequence signatures during evolution

(2015) Gustavo Parisi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Allostery without a conformational change? Revisiting the paradigm

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Decoy Database Improvement for Protein Folding

(2015) Hsin-Yi (Cindy) Yeh et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Mistranslation drives the evolution of robustness in TEM-1 β-lactamase

(2015) Sinisa Bratulic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insights into the intertwined dimer of fyn SH2

(2015) Radu Huculeci et al.   PROTEIN SCIENCE

GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands

(2015) Florent Lassalle et al.   PLoS Genetics

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

The Influence of Selection for Protein Stability on dN/dS Estimations

(2014) Pouria Dasmeh et al.   Genome Biology and Evolution

Population Size Dependence of Fitness Effect Distribution and Substitution Rate Probed by Biophysical Model of Protein Thermostability

(2013) Richard A. Goldstein   Genome Biology and Evolution

Detecting selection for negative design in proteins through an improved model of the misfolded state

(2013) Jonas Minning et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses

(2013) Angelo Pavesi et al.   PLoS Computational Biology

A Phylogenetic Analysis of Normal Modes Evolution in Enzymes and Its Relationship to Enzyme Function

(2012) Jason Lai et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Conformational Diversity Modulates Sequence Divergence

(2012) Ezequiel Juritz et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

(2012) E. D. Levy 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

Why are the low-energy protein normal modes evolutionarily conserved?

(2012) Julian Echave   PURE AND APPLIED CHEMISTRY

Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors

(2012) Geeta N. Eick et al.   PLoS Genetics

Biophysical and structural considerations for protein sequence evolution

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

Intrinsically disordered proteins: regulation and disease

(2011) M Madan Babu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A De Novo Protein Binding Pair By Computational Design and Directed Evolution

(2011) John Karanicolas et al.   MOLECULAR CELL

Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions

(2011) Adam M. Szalkowski et al.   PLoS One

Algorithm discovery by protein folding game players

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

Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy

(2011) D. A. Liberles et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint

(2011) Jessica Siltberg-Liberles et al.   Genes

Protein binding specificity versus promiscuity

(2010) Gideon Schreiber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exposure of Hydrophobic Surfaces Initiates Aggregation of Diverse ALS-Causing Superoxide Dismutase-1 Mutants

(2010) Christian Münch et al.   JOURNAL OF MOLECULAR BIOLOGY

Statistical Potentials for Improved Structurally Constrained Evolutionary Models

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

Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses

(2010) Aqeel Ahmed et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm

(2010) Enrique Marcos et al.   PLoS Computational Biology

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence

(2009) Tobias Warnecke et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins

(2009) Orly Noivirt-Brik et al.   PLoS Computational Biology

The look-ahead effect of phenotypic mutations

(2008) Dion J Whitehead et al.   Biology Direct

A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules

(2008) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

Evolutionary conservation of protein vibrational dynamics

(2008) Sandra Maguid et al.   GENE

Natural Selection against Protein Aggregation on Self-Interacting and Essential Proteins in Yeast, Fly, and Worm

(2008) Y. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences

(2008) Ugo Bastolla et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS