{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T17:08:08Z","timestamp":1765040888919},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,12,1]],"date-time":"2018-12-01T00:00:00Z","timestamp":1543622400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2583-6","type":"journal-article","created":{"date-parts":[[2018,12,29]],"date-time":"2018-12-29T10:36:08Z","timestamp":1546079768000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["hoDCA: higher order direct-coupling analysis"],"prefix":"10.1186","volume":"19","author":[{"given":"Michael","family":"Schmidt","sequence":"first","affiliation":[]},{"given":"Kay","family":"Hamacher","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,12,29]]},"reference":[{"key":"2583_CR1","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1146\/annurev.bb.25.060196.000553","volume":"25","author":"B Rost","year":"1996","unstructured":"Rost B, Sander C. Bridging the protein sequence-structure gap by structure predictions. Ann Rev Biophys Biomol Struct. 1996; 25:113\u201336.","journal-title":"Ann Rev Biophys Biomol Struct"},{"key":"2583_CR2","doi-asserted-by":"publisher","unstructured":"Yang J, Zhang Y. Protein Structure and Function Prediction Using I-TASSER. Curr Protoc Bioinforma. 2015; 52:5.8.1\u201315. \n                    https:\/\/doi.org\/10.1002\/0471250953.bi0508s52\n                    \n                  .","DOI":"10.1002\/0471250953.bi0508s52"},{"key":"2583_CR3","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1021\/bi902153g","volume":"49","author":"KW Kaufmann","year":"2010","unstructured":"Kaufmann KW, Lemmon GH, DeLuca SL, Sheehan JH, Meiler J. Practically useful: What the rosetta protein modeling suite can do for you. Biochemistry. 2010; 49:2987\u201398.","journal-title":"Biochemistry"},{"key":"2583_CR4","doi-asserted-by":"publisher","unstructured":"Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Improving physical realism, stereochemistry and side-chain accuracy in homology modeling: four approaches that performed well in CASP8. Proteins. 2009; 77:114\u201322. \n                    https:\/\/doi.org\/10.1002\/prot.22570\n                    \n                  .","DOI":"10.1002\/prot.22570"},{"key":"2583_CR5","doi-asserted-by":"publisher","unstructured":"Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Identification of direct residue contacts in protein\u2013protein interaction by message passing. Proc Natl Acad Sci. 2009; 106(1):67\u201372. \n                    https:\/\/doi.org\/10.1073\/pnas.0805923106\n                    \n                  . \n                    http:\/\/www.pnas.org\/content\/106\/1\/67.full.pdf\n                    \n                  .","DOI":"10.1073\/pnas.0805923106"},{"key":"2583_CR6","doi-asserted-by":"publisher","unstructured":"Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci. 2011; 108(49):1293\u2013301. \n                    https:\/\/doi.org\/10.1073\/pnas.1111471108\n                    \n                  . \n                    http:\/\/www.pnas.org\/content\/108\/49\/E1293.full.pdf\n                    \n                  .","DOI":"10.1073\/pnas.1111471108"},{"key":"2583_CR7","doi-asserted-by":"publisher","unstructured":"Ekeberg M, L\u00f6vkvist C, Lan Y, Weigt M, Aurell E. Improved contact prediction in proteins: Using pseudolikelihoods to infer potts models. Phys Rev E. 2013; 87:012707. \n                    https:\/\/doi.org\/10.1103\/PhysRevE.87.012707\n                    \n                  .","DOI":"10.1103\/PhysRevE.87.012707"},{"key":"2583_CR8","doi-asserted-by":"publisher","unstructured":"Ekeberg M, Hartonen T, Aurell E. Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences. J Comput Phys. 2014; 276:341\u201356. \n                    https:\/\/doi.org\/10.1016\/j.jcp.2014.07.024\n                    \n                  .","DOI":"10.1016\/j.jcp.2014.07.024"},{"key":"2583_CR9","doi-asserted-by":"publisher","unstructured":"Baldassi C, Zamparo M, Feinauer C, Procaccini A, Zecchina R, Weigt M, Pagnani A. Fast and accurate multivariate gaussian modeling of protein families: Predicting residue contacts and protein-interaction partners. PLoS ONE. 2014; 9(3):1\u201312. \n                    https:\/\/doi.org\/10.1371\/journal.pone.0092721\n                    \n                  .","DOI":"10.1371\/journal.pone.0092721"},{"key":"2583_CR10","doi-asserted-by":"publisher","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. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btr638\n                    \n                  . \n                    http:\/\/bioinformatics.oxfordjournals.org\/content\/28\/2\/184.full.pdf+html\n                    \n                  .","DOI":"10.1093\/bioinformatics\/btr638"},{"key":"2583_CR11","doi-asserted-by":"publisher","unstructured":"Stein RR, Marks DS, Sander C. Inferring pairwise interactions from biological data using maximum-entropy probability models. PLoS Comput Biol. 2015; 11(7):1\u201322. \n                    https:\/\/doi.org\/10.1371\/journal.pcbi.1004182\n                    \n                  .","DOI":"10.1371\/journal.pcbi.1004182"},{"key":"2583_CR12","doi-asserted-by":"publisher","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. 2015; 31(7):999. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btu791\n                    \n                  .","DOI":"10.1093\/bioinformatics\/btu791"},{"key":"2583_CR13","doi-asserted-by":"publisher","unstructured":"Sheridan R, Fieldhouse RJ, Hayat S, Sun Y, Antipin Y, Yang L, Hopf T, Marks DS, Sander C. Evfold.org: Evolutionary couplings and protein 3d structure prediction. bioRxiv. 2015. \n                    https:\/\/doi.org\/10.1101\/021022\n                    \n                  . \n                    http:\/\/www.biorxiv.org\/content\/early\/2015\/07\/02\/021022.full.pdf\n                    \n                  .","DOI":"10.1101\/021022"},{"key":"2583_CR14","doi-asserted-by":"publisher","unstructured":"Skwark MJ, Raimondi D, Michel M, Elofsson A. Improved contact predictions using the recognition of protein like contact patterns. PLoS Comput Biol. 2014; 10(11):1\u201314. \n                    https:\/\/doi.org\/10.1371\/journal.pcbi.1003889\n                    \n                  .","DOI":"10.1371\/journal.pcbi.1003889"},{"key":"2583_CR15","doi-asserted-by":"publisher","unstructured":"Schmidt M, Hamacher K. Three-body interactions improve contact prediction within direct-coupling analysis. Phys Rev E. 2017; 96:052405. \n                    https:\/\/doi.org\/10.1103\/PhysRevE.96.052405\n                    \n                  .","DOI":"10.1103\/PhysRevE.96.052405"},{"key":"2583_CR16","doi-asserted-by":"publisher","unstructured":"Bezanson J, Edelman A, Karpinski S, Shah VB. Julia: A fresh approach to numerical computing. SIAM Rev. 2017; 59(1):65\u201398. \n                    https:\/\/doi.org\/10.1137\/141000671\n                    \n                  .","DOI":"10.1137\/141000671"},{"key":"2583_CR17","unstructured":"Baldassi C. \n                    https:\/\/github.com\/carlobaldassi\/argparse.jl\n                    \n                  ."},{"key":"2583_CR18","doi-asserted-by":"publisher","unstructured":"Baldassi C, Pagnani A, Weigt M, Feinauer C, Procaccini A, Zecchina R, Zamparo M. GaussDCA.jl - First release. 2014. \n                    https:\/\/doi.org\/10.5281\/zenodo.10814\n                    \n                  . \n                    https:\/\/github.com\/carlobaldassi\/GaussDCA.jl\n                    \n                  .","DOI":"10.5281\/zenodo.10814"},{"issue":"3","key":"2583_CR19","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1145\/502807.502808","volume":"33","author":"E Ch\u00e1vez","year":"2001","unstructured":"Ch\u00e1vez E, Navarro G, Baeza-Yates R, Marroqu\u00edn JL. Searching in metric spaces. ACM Comput Surv. 2001; 33(3):273\u2013321.","journal-title":"ACM Comput Surv"},{"key":"2583_CR20","doi-asserted-by":"publisher","unstructured":"Feinauer C, Skwark MJ, Pagnani A, Aurell E. Improving contact prediction along three dimensions. PLoS Comput Biol. 2014; 10(10):1\u201313. \n                    https:\/\/doi.org\/10.1371\/journal.pcbi.1003847\n                    \n                  .","DOI":"10.1371\/journal.pcbi.1003847"},{"key":"2583_CR21","doi-asserted-by":"publisher","unstructured":"Dunn SD, Wahl LM, Gloor GB. Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics. 2008; 24(3):333\u201340. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btm604\n                    \n                  . \n                    http:\/\/bioinformatics.oxfordjournals.org\/content\/24\/3\/333.full.pdf+html\n                    \n                  .","DOI":"10.1093\/bioinformatics\/btm604"},{"key":"2583_CR22","doi-asserted-by":"publisher","unstructured":"Waechter M, Jaeger K, Weissgraeber S, Widmer S, Goesele M, Hamacher K. Information-theoretic analysis of molecular (co)evolution using graphics processing units. In: Proceedings of the 3rd International Workshop on Emerging Computational Methods for the Life Sciences. ECMLS \u201912. New York, NY, USA: ACM: 2012. p. 49\u201358. \n                    https:\/\/doi.org\/10.1145\/2483954.2483963\n                    \n                  . \n                    http:\/\/doi.acm.org\/10.1145\/2483954.2483963\n                    \n                  .","DOI":"10.1145\/2483954.2483963"},{"key":"2583_CR23","doi-asserted-by":"publisher","unstructured":"Waechter M, Jaeger K, Thuerck D, Weissgraeber S, Widmer S, Goesele M, Hamacher K. Using graphics processing units to investigate molecular coevolution. Concurr Comput Pract Experience. 2014; 26(6):1278\u201396. \n                    https:\/\/doi.org\/10.1002\/cpe.3074\n                    \n                  .","DOI":"10.1002\/cpe.3074"},{"key":"2583_CR24","doi-asserted-by":"publisher","unstructured":"Grantham R. Amino acid difference formula to help explain protein evolution. Science. 1974; 185(4154):862\u20134. \n                    https:\/\/doi.org\/10.1126\/science.185.4154.862\n                    \n                  . \n                    http:\/\/science.sciencemag.org\/content\/185\/4154\/862.full.pdf\n                    \n                  .","DOI":"10.1126\/science.185.4154.862"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2583-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2583-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2583-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,12,29]],"date-time":"2019-12-29T00:04:37Z","timestamp":1577577877000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2583-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12]]},"references-count":24,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2583"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2583-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12]]},"assertion":[{"value":"18 March 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 December 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 December 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":"546"}}