Evolution-Based Functional Decomposition of Proteins

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Allosteric Communication Pathways and Thermal Rectification in PDZ-2 Protein: A Computational Study

(2015) Germán A. Miño-Galaz   JOURNAL OF PHYSICAL CHEMISTRY B

Integrative, dynamic structural biology at atomic resolution—it's about time

(2015) Henry van den Bedem et al.   NATURE METHODS

Protein Sectors: Statistical Coupling Analysis versus Conservation

(2015) Tiberiu Teşileanu et al.   PLoS Computational Biology

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

Inverse Ising inference with correlated samples

(2014) Benedikt Obermayer et al.   NEW JOURNAL OF PHYSICS

Discovering Communities through Friendship

(2014) Greg Morrison et al.   PLoS One

Conservation Weighting Functions Enable Covariance Analyses to Detect Functionally Important Amino Acids

(2014) Lucy J. Colwell et al.   PLoS One

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

(2013) Gira Bhabha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Elements of Coevolution in Biological Sequences

(2013) Olivier Rivoire   PHYSICAL REVIEW LETTERS

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction

(2013) Simona Cocco et al.   PLoS Computational Biology

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

The spatial architecture of protein function and adaptation

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

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Hot Spots for Allosteric Regulation on Protein Surfaces

(2011) Kimberly A. Reynolds et al.   CELL

Asymmetric network connectivity using weighted harmonic averages

(2011) Greg Morrison et al.   EPL

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

An interdomain sector mediating allostery in Hsp70 molecular chaperones

(2010) Robert G Smock et al.   Molecular Systems Biology

Relationship between sequence conservation and three-dimensional structure in a large family of esterases, lipases, and related proteins

(2010) Miroslaw Cygler et al.   PROTEIN SCIENCE

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Sending Signals Dynamically

(2009) R. G. Smock et al.   SCIENCE

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH