Constructing sequence-dependent protein models using coevolutionary information

Evolution, energy landscapes and the paradoxes of protein folding

(2015) Peter G. Wolynes   BIOCHIMIE

Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding

(2015) Tao Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A many-body term improves the accuracy of effective potentials based on protein coevolutionary data

(2015) A. Contini et al.   JOURNAL OF CHEMICAL PHYSICS

Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

(2015) Heiko Lammert et al.   JOURNAL OF CHEMICAL PHYSICS

Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins

(2015) Tao Chen et al.   PLoS Computational Biology

Learning To Fold Proteins Using Energy Landscape Theory

(2014) Nicholas P. Schafer et al.   ISRAEL JOURNAL OF CHEMISTRY

Biophysics of protein evolution and evolutionary protein biophysics

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

Inverse Ising inference with correlated samples

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

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

From structure to function: the convergence of structure based models and co-evolutionary information

(2014) Biman Jana et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Predictive energy landscapes for folding  -helical transmembrane proteins

(2014) B. L. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

(2014) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design

(2013) Andrew L. Ferguson et al.   IMMUNITY

The network of stabilizing contacts in proteins studied by coevolutionary data

(2013) Sara Lui et al.   JOURNAL OF CHEMICAL PHYSICS

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing

(2012) Aram Davtyan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Statistical mechanics for natural flocks of birds

(2012) W. Bialek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

(2012) A. E. Dago et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive energy landscapes for protein-protein association

(2012) W. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biomolecular dynamics: order–disorder transitions and energy landscapes

(2012) Paul C Whitford et al.   REPORTS ON PROGRESS IN PHYSICS

The Dominant Folding Route Minimizes Backbone Distortion in SH3

(2012) Heiko Lammert et al.   PLoS Computational Biology

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease

(2012) Omar Haq et al.   PLoS Computational Biology

Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks

(2011) Andrea Procaccini et al.   PLoS One

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

(2011) Wenfei Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

(2010) Jeffrey K. Noel et al.   NUCLEIC ACIDS RESEARCH

Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins

(2010) Z. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

(2009) Omar Haq et al.   BMC BIOINFORMATICS

High-resolution protein complexes from integrating genomic information with molecular simulation

(2009) Alexander Schug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robustness and generalization of structure-based models for protein folding and function

(2009) Heiko Lammert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Changes of Protein Folding Pathways by Circular Permutation

(2008) Ellinor Haglund et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

(2008) S. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

(2008) A. Zarrine-Afsar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS