{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T11:55:11Z","timestamp":1778759711624,"version":"3.51.4"},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,1,25]],"date-time":"2018-01-25T00:00:00Z","timestamp":1516838400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2018,1,25]],"date-time":"2018-01-25T00:00:00Z","timestamp":1516838400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01GM093123"],"award-info":[{"award-number":["R01GM093123"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2032-6","type":"journal-article","created":{"date-parts":[[2018,1,24]],"date-time":"2018-01-24T20:21:11Z","timestamp":1516825271000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":73,"title":["CONFOLD2: improved contact-driven ab initio protein structure modeling"],"prefix":"10.1186","volume":"19","author":[{"given":"Badri","family":"Adhikari","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianlin","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,1,25]]},"reference":[{"issue":"S1","key":"2032_CR1","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1002\/prot.24943","volume":"84","author":"B Monastyrskyy","year":"2016","unstructured":"Monastyrskyy B, D\u2019Andrea D, Fidelis K, Tramontano A, Kryshtafovych A. New encouraging developments in contact prediction: Assessment of the CASP11 results. Proteins Struct Funct Bioinforma. 2016; 84(S1):131\u201344.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"2032_CR2","doi-asserted-by":"crossref","unstructured":"Michel M, Hurtado DM, Uziela K, Elofsson A. Large-scale structure prediction by improved contact predictions and model quality assessment. bioRxiv. 2017;128231.","DOI":"10.1101\/128231"},{"issue":"8","key":"2032_CR3","doi-asserted-by":"publisher","first-page":"1436","DOI":"10.1002\/prot.24829","volume":"83","author":"B Adhikari","year":"2015","unstructured":"Adhikari B, Bhattacharya D, Cao R, Cheng J. CONFOLD: Residue-residue contact-guided ab initio protein folding. Proteins. 2015; 83(8):1436\u201349.","journal-title":"Proteins"},{"issue":"1","key":"2032_CR4","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/protein\/2.1.27","volume":"2","author":"M Nilges","year":"1988","unstructured":"Nilges M, Gronenborn AM, Br\u00fcnger AT, Clore GM. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng Des Sel. 1988; 2(1):27\u201338.","journal-title":"Protein Eng Des Sel"},{"issue":"17","key":"2032_CR5","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1093\/bioinformatics\/btu458","volume":"30","author":"M Michel","year":"2014","unstructured":"Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. Pconsfold: improved contact predictions improve protein models. Bioinformatics. 2014; 30(17):482\u20138.","journal-title":"Bioinformatics"},{"issue":"3","key":"2032_CR6","doi-asserted-by":"publisher","first-page":"e92197","DOI":"10.1371\/journal.pone.0092197","volume":"9","author":"T Kosciolek","year":"2014","unstructured":"Kosciolek T, Jones DT. De novo structure prediction of globular proteins aided by sequence variation-derived contacts. PLoS ONE. 2014; 9(3):e92197.","journal-title":"PLoS ONE"},{"issue":"S1","key":"2032_CR7","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1002\/prot.24950","volume":"84","author":"M Mabrouk","year":"2016","unstructured":"Mabrouk M, Werner T, Schneider M, Putz I, Brock O. Analysis of free modeling predictions by rbo aleph in casp11. Proteins Struct Funct Bioinforma. 2016; 84(S1):87\u2013104.","journal-title":"Proteins Struct Funct Bioinforma"},{"issue":"1","key":"2032_CR8","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/protein\/2.1.27","volume":"2","author":"M Nilges","year":"1988","unstructured":"Nilges M, Gronenborn AM, Br\u00fcnger AT, Clore GM. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng Des Sel. 1988; 2(1):27\u201338.","journal-title":"Protein Eng Des Sel"},{"issue":"Web Server","key":"2032_CR9","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1093\/nar\/gki396","volume":"33","author":"J Cheng","year":"2005","unstructured":"Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 2005; 33(Web Server):72\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"2032_CR10","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1093\/bioinformatics\/16.9.776","volume":"16","author":"N Siew","year":"2000","unstructured":"Siew N, Elofsson A, Rychlewski L, Fischer D. Maxsub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics. 2000; 16(9):776\u201385.","journal-title":"Bioinformatics"},{"issue":"2","key":"2032_CR11","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1093\/bioinformatics\/btr638","volume":"28","author":"DT Jones","year":"2012","unstructured":"Jones DT, Buchan DWA, Cozzetto D, Pontil M. Psicov: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 2012; 28(2):184\u201390.","journal-title":"Bioinformatics"},{"issue":"1","key":"2032_CR12","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1186\/s12859-016-1404-z","volume":"17","author":"B Adhikari","year":"2016","unstructured":"Adhikari B, Nowotny J, Bhattacharya D, Hou J, Cheng J. Coneva: a toolbox for comprehensive assessment of protein contacts. BMC Bioinformatics. 2016; 17(1):517.","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"2032_CR13","first-page":"791","volume":"31","author":"DT Jones","year":"2014","unstructured":"Jones DT, Singh T, Kosciolek T, Tetchner S. MetaPSICOV: Combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics. 2014; 31(7):791.","journal-title":"Bioinformatics"},{"issue":"17","key":"2032_CR14","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1093\/bioinformatics\/btu458","volume":"30","author":"M Michel","year":"2014","unstructured":"Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. Pconsfold: improved contact predictions improve protein models. Bioinformatics. 2014; 30(17):482\u20138.","journal-title":"Bioinformatics"},{"issue":"3","key":"2032_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0092197","volume":"9","author":"T Kosciolek","year":"2014","unstructured":"Kosciolek T, Jones DT. De novo structure prediction of globular proteins aided by sequence variation-derived contacts. PLOS ONE. 2014; 9(3):1\u201315.","journal-title":"PLOS ONE"},{"issue":"S1","key":"2032_CR16","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1002\/prot.24863","volume":"84","author":"T Kosciolek","year":"2016","unstructured":"Kosciolek T, Jones DT. Accurate contact predictions using covariation techniques and machine learning. Proteins Struct Funct Bioinforma. 2016; 84(S1):145\u201351.","journal-title":"Proteins Struct Funct Bioinforma"},{"issue":"00","key":"2032_CR17","first-page":"000","volume":"00","author":"S Wang","year":"2017","unstructured":"Wang S, Sun S, Xu J. Analysis of deep learning methods for blind protein contact prediction in casp12. Proteins Struct Funct Bioinforma. 2017; 00(00):000\u2013000.","journal-title":"Proteins Struct Funct Bioinforma"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2032-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2032-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2032-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T07:02:16Z","timestamp":1589439736000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2032-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,1,25]]},"references-count":17,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2032"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2032-6","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/228460","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,25]]},"assertion":[{"value":"19 November 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 January 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 January 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"22"}}