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

Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1

(2014) S. Tamir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure of the entire respiratory complex I

(2013) Rozbeh Baradaran et al.   NATURE

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

Correction for Kamisetty et al., Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

(2013) Raghavendra Hosur et al.   GENOME BIOLOGY

MESSA: MEta-Server for protein Sequence Analysis

(2012) Qian Cong et al.   BMC BIOLOGY

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

The Antibiotic Thermorubin Inhibits Protein Synthesis by Binding to Inter-Subunit Bridge B2a of the Ribosome

(2012) David Bulkley et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter

(2012) Romina Mancusso et al.   NATURE

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

EcoGene 3.0

(2012) Jindan Zhou et al.   NUCLEIC ACIDS RESEARCH

Structure and mechanism of the tripartite CusCBA heavy-metal efflux complex

(2012) F. Long et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

(2012) T. Nugent 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

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

(2012) O. F. Lange 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

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

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

Structural basis for gating charge movement in the voltage sensor of a sodium channel

(2011) V. Yarov-Yarovoy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition

(2011) Eric Johnson et al.   PROTEIN SCIENCE

Studying the co-evolution of protein families with the Mirrortree web server

(2010) David Ochoa et al.   BIOINFORMATICS

Crystal structure of toll-like receptor 2-activating lipoprotein IIpA from Vibrio vulnificus

(2010) Sangheon Yu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Learning generative models for protein fold families

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

Crystal Structure of the Periplasmic Component of a Tripartite Macrolide-Specific Efflux Pump

(2009) Soohwan Yum et al.   JOURNAL OF MOLECULAR BIOLOGY

Berkeley PHOG: PhyloFacts orthology group prediction web server

(2009) Ruchira S. Datta et al.   NUCLEIC ACIDS RESEARCH

Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition

(2009) Akiyoshi Nakamura et al.   NUCLEIC ACIDS RESEARCH

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 prediction for CASP8 with all-atom refinement using Rosetta

(2009) Srivatsan Raman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Graphical Models of Residue Coupling in Protein Families

(2008) J. Thomas et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

(2008) Lukas Burger et al.   Molecular Systems Biology

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

Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme

(2008) J. L. Vey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA