From residue coevolution to protein conformational ensembles and functional dynamics

A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases

(2015) Raju Kalaivani et al.   Molecular BioSystems

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

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

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

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

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

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of residue-residue contact prediction in CASP10

(2013) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Ras protein superfamily: Evolutionary tree and role of conserved amino acids

(2012) Ana Maria Rojas et al.   JOURNAL OF CELL BIOLOGY

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties

(2012) Marco Pasi et al.   Journal of Chemical Theory and Computation

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

Genomics-aided structure prediction

(2012) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) David T. Jones et al.   BIOINFORMATICS

A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions

(2011) Ludovico Sutto et al.   Journal of Chemical Theory and Computation

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

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

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2010) Lukas Burger et al.   PLoS Computational Biology

Lymphotactin: How a protein can adopt two folds

(2009) Carlo Camilloni et al.   JOURNAL OF CHEMICAL PHYSICS

Fundamental Link between Folding States and Functional States of Proteins

(2009) Hans Robert Kalbitzer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ising model for neural data: Model quality and approximate methods for extracting functional connectivity

(2009) Yasser Roudi et al.   PHYSICAL REVIEW E

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

Structure and Signaling Mechanism of Per-ARNT-Sim Domains

(2009) Andreas Möglich et al.   STRUCTURE

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

Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding

(2007) Young C. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY