{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T22:47:25Z","timestamp":1776379645120,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005324","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,1,20]],"date-time":"2017-01-20T00:00:00Z","timestamp":1484870400000}}],"reference-count":49,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2017,1,5]],"date-time":"2017-01-05T00:00:00Z","timestamp":1483574400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM089753"],"award-info":[{"award-number":["R01GM089753"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000076","name":"Directorate for Biological Sciences","doi-asserted-by":"publisher","award":["DBI-1564955"],"award-info":[{"award-number":["DBI-1564955"]}],"id":[{"id":"10.13039\/100000076","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005324","type":"journal-article","created":{"date-parts":[[2017,1,9]],"date-time":"2017-01-09T14:57:34Z","timestamp":1483973854000},"page":"e1005324","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":881,"title":["Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model"],"prefix":"10.1371","volume":"13","author":[{"given":"Sheng","family":"Wang","sequence":"first","affiliation":[]},{"given":"Siqi","family":"Sun","sequence":"additional","affiliation":[]},{"given":"Zhen","family":"Li","sequence":"additional","affiliation":[]},{"given":"Renyu","family":"Zhang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7111-4839","authenticated-orcid":true,"given":"Jinbo","family":"Xu","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2017,1,5]]},"reference":[{"issue":"S2","key":"ref1","first-page":"208","article-title":"One contact for every twelve residues allows robust and accurate topology\u2010level protein structure modeling. Proteins: Structure, Function, and","volume":"82","author":"DE Kim","year":"2014","journal-title":"Bioinformatics"},{"issue":"4","key":"ref2","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/nrg3414","article-title":"Emerging methods in protein co-evolution","volume":"14","author":"D de Juan","year":"2013","journal-title":"Nature Reviews Genetics"},{"issue":"1","key":"ref3","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":"P Natl Acad Sci USA"},{"issue":"21","key":"ref4","doi-asserted-by":"crossref","first-page":"3128","DOI":"10.1093\/bioinformatics\/btu500","article-title":"CCMpred\u2014fast and precise prediction of protein residue\u2013residue contacts from correlated mutations","volume":"30","author":"S Seemayer","year":"2014","journal-title":"Bioinformatics"},{"issue":"2","key":"ref5","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"},{"issue":"12","key":"ref6","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":"ref7","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.jcp.2014.07.024","article-title":"Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences","volume":"276","author":"M Ekeberg","year":"2014","journal-title":"J Comput Phys"},{"issue":"39","key":"ref8","doi-asserted-by":"crossref","first-page":"15674","DOI":"10.1073\/pnas.1314045110","article-title":"Assessing the utility of coevolution-based residue\u2013residue contact predictions in a sequence-and structure-rich era","volume":"110","author":"H Kamisetty","year":"2013","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"7","key":"ref9","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1093\/bioinformatics\/btu791","article-title":"MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins","volume":"31","author":"DT Jones","year":"2015","journal-title":"Bioinformatics"},{"key":"ref10","article-title":"Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning","author":"J Ma","year":"2015","journal-title":"Bioinformatics"},{"issue":"8","key":"ref11","first-page":"1436","article-title":"CONFOLD: residue\u2010residue contact\u2010guided ab initio protein folding. Proteins: Structure, Function, and","volume":"83","author":"B Adhikari","year":"2015","journal-title":"Bioinformatics"},{"key":"ref12","article-title":"CoinFold: a web server for protein contact prediction and contact-assisted protein folding","author":"S Wang","year":"2016","journal-title":"Nucleic acids research"},{"issue":"19","key":"ref13","doi-asserted-by":"crossref","first-page":"2449","DOI":"10.1093\/bioinformatics\/bts475","article-title":"Deep architectures for protein contact map prediction","volume":"28","author":"P Di Lena","year":"2012","journal-title":"Bioinformatics"},{"issue":"1","key":"ref14","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"},{"issue":"4","key":"ref15","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 G\u00f6bel","year":"1994","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"issue":"49","key":"ref16","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":"Proceedings of the National Academy of Sciences"},{"issue":"11","key":"ref17","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"},{"issue":"7","key":"ref18","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1093\/bioinformatics\/btn069","article-title":"A comprehensive assessment of sequence-based and template-based methods for protein contact prediction","volume":"24","author":"S Wu","year":"2008","journal-title":"Bioinformatics"},{"issue":"13","key":"ref19","doi-asserted-by":"crossref","first-page":"i266","DOI":"10.1093\/bioinformatics\/btt211","article-title":"Predicting protein contact map using evolutionary and physical constraints by integer programming","volume":"29","author":"Z Wang","year":"2013","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","unstructured":"He K, Zhang X, Ren S, Sun J. Deep residual learning for image recognition. arXiv preprint arXiv:151203385. 2015.","DOI":"10.1109\/CVPR.2016.90"},{"key":"ref21","unstructured":"Krizhevsky A, Hinton G. Convolutional deep belief networks on cifar-10. Unpublished manuscript. 2010;40."},{"key":"ref22","article-title":"Training very deep networks","author":"RK Srivastava","year":"2015"},{"issue":"6","key":"ref23","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1109\/MSP.2012.2205597","article-title":"Deep neural networks for acoustic modeling in speech recognition: The shared views of four research groups","volume":"29","author":"G Hinton","year":"2012","journal-title":"IEEE Signal Processing Magazine"},{"issue":"7553","key":"ref24","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nature14539","article-title":"Deep learning","volume":"521","author":"Y LeCun","year":"2015","journal-title":"Nature"},{"key":"ref25","doi-asserted-by":"crossref","unstructured":"Szegedy C, Liu W, Jia Y, Sermanet P, Reed S, Anguelov D, et al., editors. Going deeper with convolutions. Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition; 2015.","DOI":"10.1109\/CVPR.2015.7298594"},{"issue":"S2","key":"ref26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/prot.24452","article-title":"Critical assessment of methods of protein structure prediction (CASP)\u2014round x","volume":"82","author":"J Moult","year":"2014","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"ref27","article-title":"Critical assessment of methods of protein structure prediction: Progress and new directions in round XI","author":"J Moult","year":"2016","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"ref28","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bat031","article-title":"The Protein Model Portal\u2014a comprehensive resource for protein structure and model information","volume":"2013","author":"J Haas","year":"2013","journal-title":"Database"},{"key":"ref29","article-title":"Recurrent Convolutional Neural Networks for Scene Labeling","author":"PH Pinheiro","year":"2014"},{"key":"ref30","unstructured":"Nair V, Hinton GE, editors. Rectified linear units improve restricted boltzmann machines. Proceedings of the 27th International Conference on Machine Learning (ICML-10); 2010."},{"key":"ref31","article-title":"New encouraging developments in contact prediction: Assessment of the CASP11 results","author":"B Monastyrskyy","year":"2015","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"issue":"5","key":"ref32","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1107\/S0907444998003254","article-title":"Crystallography &amp; NMR system: A new software suite for macromolecular structure determination","volume":"54","author":"AT Briinger","year":"1998","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"4","key":"ref33","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: Structure, Function, and Bioinformatics"},{"issue":"7","key":"ref34","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btq066","article-title":"How significant is a protein structure similarity with TM-score = 0.5?","volume":"26","author":"JR Xu","year":"2010","journal-title":"Bioinformatics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gkh468","article-title":"Protein structure prediction and analysis using the Robetta server","volume":"32","author":"DE Kim","year":"2004","journal-title":"Nucleic Acids Research"},{"issue":"6","key":"ref36","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"LA Kelley","year":"2015","journal-title":"Nature protocols"},{"issue":"8","key":"ref37","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1038\/nprot.2012.085","article-title":"Template-based protein structure modeling using the RaptorX web server","volume":"7","author":"M K\u00e4llberg","year":"2012","journal-title":"Nature protocols"},{"issue":"W1","key":"ref38","doi-asserted-by":"crossref","first-page":"W252","DOI":"10.1093\/nar\/gku340","article-title":"SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information","volume":"42","author":"M Biasini","year":"2014","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"ref39","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nmeth.1818","article-title":"HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment","volume":"9","author":"M Remmert","year":"2012","journal-title":"Nature methods"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1448","DOI":"10.1038\/srep01448","article-title":"Protein structure alignment beyond spatial proximity","volume":"3","author":"S Wang","year":"2013","journal-title":"Sci Rep"},{"key":"ref41","article-title":"Structure of the Shroom-Rho kinase complex reveals a binding interface with monomeric Shroom that regulates cell morphology and stimulates kinase activity","author":"JK Zalewski","year":"2016","journal-title":"J Biol Chem"},{"issue":"11","key":"ref42","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1091\/mbc.E11-11-0937","article-title":"Structure of Shroom domain 2 reveals a three-segmented coiled-coil required for dimerization, Rock binding, and apical constriction","volume":"23","author":"S Mohan","year":"2012","journal-title":"Mol Biol Cell"},{"key":"ref43","unstructured":"Ioffe S, Szegedy C, editors. Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift. Proceedings of The 32nd International Conference on Machine Learning; 2015."},{"key":"ref44","doi-asserted-by":"crossref","DOI":"10.1038\/srep18962","article-title":"Protein secondary structure prediction using deep convolutional neural fields","volume":"6","author":"S Wang","year":"2016","journal-title":"Sci Rep"},{"issue":"3","key":"ref45","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1021\/ma00145a039","article-title":"Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation","volume":"18","author":"S Miyazawa","year":"1985","journal-title":"Macromolecules"},{"issue":"02","key":"ref46","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1110\/ps.8.2.361","article-title":"Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes","volume":"8","author":"MR Betancourt","year":"1999","journal-title":"Protein Science"},{"key":"ref47","doi-asserted-by":"crossref","unstructured":"Bergstra J, Breuleux O, Bastien F, Lamblin P, Pascanu R, Desjardins G, et al., editors. Theano: A CPU and GPU math compiler in Python. Proc 9th Python in Science Conf; 2010.","DOI":"10.25080\/Majora-92bf1922-003"},{"key":"ref48","article-title":"JPred4: a protein secondary structure prediction server","author":"A Drozdetskiy","year":"2015","journal-title":"Nucleic acids research"},{"key":"ref49","article-title":"RaptorX-Property: a web server for protein structure property prediction","author":"S Wang","year":"2016","journal-title":"Nucleic acids research"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005324","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,1,20]],"date-time":"2017-01-20T00:00:00Z","timestamp":1484870400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005324","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,28]],"date-time":"2020-09-28T15:21:46Z","timestamp":1601306506000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005324"}},"subtitle":[],"editor":[{"given":"Avner","family":"Schlessinger","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,1,5]]},"references-count":49,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,1,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005324","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.727169815.793534330","asserted-by":"object"}],"has-preprint":[{"id-type":"doi","id":"10.1101\/073239","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,5]]}}}