Accurate contact predictions using covariation techniques and machine learning

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

(2014) Stefan Seemayer et al.   BIOINFORMATICS

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

FreeContact: fast and free software for protein contact prediction from residue co-evolution

(2014) László Kaján et al.   BMC 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

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

Prediction of contacts from correlated sequence substitutions

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

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

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

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

(2013) David E. Kim 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

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

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

Transmembrane protein topology prediction using support vector machines

(2009) Timothy Nugent et al.   BMC 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