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

Prediction of contacts from correlated sequence substitutions

(2013) William R Taylor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

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

Genomics-aided structure prediction

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

The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future

(2012) Helen M. Berman et al.   STRUCTURE

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

(2011) David T. Jones et al.   BIOINFORMATICS

Direct correlation analysis improves fold recognition

(2011) Michael I. Sadowski et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

High-dimensional inference with the generalized Hopfield model: Principal component analysis and corrections

(2011) S. Cocco et al.   PHYSICAL REVIEW E

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

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Protein interactions and ligand binding: From protein subfamilies to functional specificity

(2010) A. Rausell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Neuronal couplings between retinal ganglion cells inferred by efficient inverse statistical physics methods

(2009) S. Cocco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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