{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T06:04:17Z","timestamp":1760853857430},"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2015,12,29]],"date-time":"2015-12-29T00:00:00Z","timestamp":1451347200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004661","type":"journal-article","created":{"date-parts":[[2015,12,29]],"date-time":"2015-12-29T18:48:21Z","timestamp":1451414901000},"page":"e1004661","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction"],"prefix":"10.1371","volume":"11","author":[{"given":"Tatjana","family":"Braun","sequence":"first","affiliation":[]},{"given":"Julia","family":"Koehler Leman","sequence":"additional","affiliation":[]},{"given":"Oliver F.","family":"Lange","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2015,12,29]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","article-title":"Principles that govern the folding of protein chains","volume":"181","author":"CB Anfinsen","year":"1973","journal-title":"Science"},{"issue":"Suppl 7","key":"ref2","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/prot.20729","article-title":"Free modeling with Rosetta in CASP6","volume":"61","author":"P Bradley","year":"2005","journal-title":"Proteins"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1126\/science.1113801","article-title":"Toward high-resolution de novo structure prediction for small proteins","volume":"309","author":"P Bradley","year":"2005","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.jmb.2009.07.063","article-title":"Sampling bottlenecks in de novo protein structure prediction","volume":"393","author":"DE Kim","year":"2009","journal-title":"J Mol Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1126\/science.1183649","article-title":"NMR structure determination for larger proteins using backbone-only data","volume":"327","author":"S Raman","year":"2010","journal-title":"Science"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"10873","DOI":"10.1073\/pnas.1203013109","article-title":"Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples","volume":"109","author":"OF Lange","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1038\/nbt.2419","article-title":"Protein structure prediction from sequence variation","volume":"30","author":"DS Marks","year":"2012","journal-title":"Nat Biotechnol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1002\/prot.340180402","article-title":"Correlated mutations and residue contacts in proteins","volume":"18","author":"U Gobel","year":"1994","journal-title":"Proteins"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/0097-8485(94)85019-4","article-title":"Sequence conservation and correlation measures in protein structure prediction","volume":"18","author":"K Hatrick","year":"1994","journal-title":"Comput Chem"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1073\/pnas.91.1.98","article-title":"How frequent are correlated changes in families of protein sequences?","volume":"91","author":"E Neher","year":"1994","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1093\/protein\/7.3.349","article-title":"Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?","volume":"7","author":"IN Shindyalov","year":"1994","journal-title":"Protein Eng"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e1000633","DOI":"10.1371\/journal.pcbi.1000633","article-title":"Disentangling direct from indirect co-evolution of residues in protein alignments","volume":"6","author":"L Burger","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"e28766","DOI":"10.1371\/journal.pone.0028766","article-title":"Protein 3D structure computed from evolutionary sequence variation","volume":"6","author":"DS Marks","year":"2011","journal-title":"PLoS One"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"E1293","DOI":"10.1073\/pnas.1111471108","article-title":"Direct-coupling analysis of residue coevolution captures native contacts across many protein families","volume":"108","author":"F Morcos","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1073\/pnas.0805923106","article-title":"Identification of direct residue contacts in protein-protein interaction by message passing","volume":"106","author":"M Weigt","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref16","article-title":"Using sequence alignments to predict protein structure and stability with high accuracy","author":"A GB Lapedes","year":"2012","journal-title":"ArXiv e-prints"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1093\/bioinformatics\/btr638","article-title":"PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments","volume":"28","author":"DT Jones","year":"2012","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"15674","DOI":"10.1073\/pnas.1314045110","article-title":"Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era","volume":"110","author":"H Kamisetty","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"012707","DOI":"10.1103\/PhysRevE.87.012707","article-title":"Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models","volume":"87","author":"M Ekeberg","year":"2013","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"3128","DOI":"10.1093\/bioinformatics\/btu500","article-title":"CCMpred\u2014fast and precise prediction of protein residue-residue contacts from correlated mutations","volume":"30","author":"S Seemayer","year":"2014","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e1003889","DOI":"10.1371\/journal.pcbi.1003889","article-title":"Improved contact predictions using the recognition of protein like contact patterns","volume":"10","author":"MJ Skwark","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"22124","DOI":"10.1073\/pnas.0912100106","article-title":"High-resolution protein complexes from integrating genomic information with molecular simulation","volume":"106","author":"A Schug","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e02030","DOI":"10.7554\/eLife.02030","article-title":"Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information","volume":"3","author":"S Ovchinnikov","year":"2014","journal-title":"Elife"},{"key":"ref24","article-title":"Sequence co-evolution gives 3D contacts and structures of protein complexes","volume":"3","author":"TA Hopf","year":"2014","journal-title":"Elife"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1016\/j.cell.2012.04.012","article-title":"Three-dimensional structures of membrane proteins from genomic sequencing","volume":"149","author":"TA Hopf","year":"2012","journal-title":"Cell"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"5413","DOI":"10.1073\/pnas.1419956112","article-title":"All-atom 3D structure prediction of transmembrane beta-barrel proteins from sequences","volume":"112","author":"S Hayat","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1107\/S0907444998003254","article-title":"Crystallography & NMR system: A new software suite for macromolecular structure determination","volume":"54","author":"AT Brunger","year":"1998","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2728","DOI":"10.1038\/nprot.2007.406","article-title":"Version 1.2 of the Crystallography and NMR system","volume":"2","author":"AT Brunger","year":"2007","journal-title":"Nat Protoc"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1002\/prot.1171","article-title":"Predicting novel protein folds by using FRAGFOLD","volume":"5","author":"DT Jones","year":"2001","journal-title":"Proteins Suppl"},{"issue":"Suppl 7","key":"ref30","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1002\/prot.20731","article-title":"Prediction of novel and analogous folds using fragment assembly and fold recognition","volume":"61","author":"DT Jones","year":"2005","journal-title":"Proteins"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e92197","DOI":"10.1371\/journal.pone.0092197","article-title":"De novo structure prediction of globular proteins aided by sequence variation-derived contacts","volume":"9","author":"T Kosciolek","year":"2014","journal-title":"PLoS One"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/S0076-6879(04)83004-0","article-title":"Protein structure prediction using Rosetta","volume":"383","author":"CA Rohl","year":"2004","journal-title":"Methods Enzymol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"i482","DOI":"10.1093\/bioinformatics\/btu458","article-title":"PconsFold: improved contact predictions improve protein models","volume":"30","author":"M Michel","year":"2014","journal-title":"Bioinformatics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.1093\/bioinformatics\/btt259","article-title":"PconsC: combination of direct information methods and alignments improves contact prediction","volume":"29","author":"MJ Skwark","year":"2013","journal-title":"Bioinformatics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1002\/prot.24829","article-title":"CONFOLD: Residue-residue contact-guided ab initio protein folding","volume":"83","author":"B Adhikari","year":"2015","journal-title":"Proteins"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1002\/prot.23245","article-title":"Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation","volume":"80","author":"OF Lange","year":"2012","journal-title":"Proteins"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1107\/S0907444902003451","article-title":"The Protein Data Bank","volume":"58","author":"HM Berman","year":"2002","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1002\/prot.22934","article-title":"Learning generative models for protein fold families","volume":"79","author":"S Balakrishnan","year":"2011","journal-title":"Proteins"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1002\/prot.340230412","article-title":"Knowledge-based protein secondary structure assignment","volume":"23","author":"D Frishman","year":"1995","journal-title":"Proteins"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1002\/prot.20264","article-title":"Scoring function for automated assessment of protein structure template quality","volume":"57","author":"Y Zhang","year":"2004","journal-title":"Proteins"},{"key":"ref42","unstructured":"Schrodinger, LLC (2010) The PyMOL Molecular Graphics System, Version 1.3r1."}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004661","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T21:03:30Z","timestamp":1540328610000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004661"}},"subtitle":[],"editor":[{"given":"Debora S","family":"Marks","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2015,12,29]]},"references-count":42,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2015,12,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004661","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,12,29]]}}}