Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction

How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins?

(2018) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inverse statistical physics of protein sequences: a key issues review

(2018) Simona Cocco et al.   REPORTS ON PROGRESS IN PHYSICS

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

Improving residue–residue contact prediction via low-rank and sparse decomposition of residue correlation matrix

(2016) Haicang Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

ACE: adaptive cluster expansion for maximum entropy graphical model inference

(2016) J. P. Barton et al.   BIOINFORMATICS

On the Entropy of Protein Families

(2016) John P. Barton et al.   JOURNAL OF STATISTICAL PHYSICS

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

(2015) Sikander Hayat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From residue coevolution to protein conformational ensembles and functional dynamics

(2015) Ludovico Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors

(2015) Thomas A. Hopf et al.   Nature Communications

Large-scale determination of previously unsolved protein structures using evolutionary information

(2015) Sergey Ovchinnikov et al.   eLife

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

(2014) Stefan Seemayer et al.   BIOINFORMATICS

Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences

(2014) Magnus Ekeberg et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

(2014) Carlo Baldassi et al.   PLoS One

De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

(2014) Tomasz Kosciolek et al.   PLoS One

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

(2014) Marcin J. Skwark et al.   PLoS Computational Biology

Improving Contact Prediction along Three Dimensions

(2014) Christoph Feinauer et al.   PLoS Computational Biology

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

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

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

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

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

(2011) David T. Jones et al.   BIOINFORMATICS

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

A new method for revealing correlated mutations under the structural and functional constraints in proteins

(2009) Byung-Chul Lee et al.   BIOINFORMATICS

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information

(2009) C. M. Buslje et al.   BIOINFORMATICS

Graphical Models of Residue Coupling in Protein Families

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

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