PT  - JOURNAL ARTICLE
AU  - Robert Sheridan
AU  - Robert J. Fieldhouse
AU  - Sikander Hayat
AU  - Yichao Sun
AU  - Yevgeniy Antipin
AU  - Li Yang
AU  - Thomas Hopf
AU  - Debora S. Marks
AU  - Chris Sander
TI  - EVfold.org: Evolutionary Couplings and Protein 3D Structure Prediction
AID  - 10.1101/021022
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 021022
4099  - http://biorxiv.org/content/early/2015/07/02/021022.short
4100  - http://biorxiv.org/content/early/2015/07/02/021022.full
AB  - Recently developed maximum entropy methods infer evolutionary constraints on protein function and structure from the millions of protein sequences available in genomic databases. The EVfold web server (at EVfold.org) makes these methods available to predict functional and structural interactions in proteins. The key algorithmic development has been to disentangle direct and indirect residue-residue correlations in large multiple sequence alignments and derive direct residue-residue evolutionary couplings (EVcouplings or ECs). For proteins of unknown structure, distance constraints obtained from evolutionarily couplings between residue pairs are used to de novo predict all-atom 3D structures, often to good accuracy. Given sufficient sequence information in a protein family, this is a major advance toward solving the problem of computing the native 3D fold of proteins from sequence information alone.Availability EVfold server at http://evfold.org/Contact evfoldtest{at}gmail.comDIdirect informationECevolutionary couplingEVevolutionaryMSAmultiple sequence alignmentPLMpseudo-likelihood maximizationPPVpositive predictive value (number of true positives divided by the sum of true and false positives)TM-scoretemplate modeling score