{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T09:39:22Z","timestamp":1778924362240,"version":"3.51.4"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2018,10,9]],"date-time":"2018-10-09T00:00:00Z","timestamp":1539043200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"GRFP","award":["DGE1144152"],"award-info":[{"award-number":["DGE1144152"]}]},{"name":"DOE CSGF","award":["DE-FG02-97ER25308"],"award-info":[{"award-number":["DE-FG02-97ER25308"]}]},{"name":"Pathway Commons","award":["U41 HG006623"],"award-info":[{"award-number":["U41 HG006623"]}]},{"name":"Pathway Commons","award":["NRNB P41 GM103504"],"award-info":[{"award-number":["NRNB P41 GM103504"]}]},{"name":"Pathway Commons","award":["R01 GM106303"],"award-info":[{"award-number":["R01 GM106303"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Coevolutionary sequence analysis has become a commonly used technique for de novo prediction of the structure and function of proteins, RNA, and protein complexes. We present the EVcouplings framework, a fully integrated open-source application and Python package for coevolutionary analysis. The framework enables generation of sequence alignments, calculation and evaluation of evolutionary couplings (ECs), and de novo prediction of structure and mutation effects. The combination of an easy to use, flexible command line interface and an underlying modular Python package makes the full power of coevolutionary analyses available to entry-level and advanced users.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/debbiemarkslab\/evcouplings<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty862","type":"journal-article","created":{"date-parts":[[2018,10,8]],"date-time":"2018-10-08T16:17:06Z","timestamp":1539015426000},"page":"1582-1584","source":"Crossref","is-referenced-by-count":303,"title":["The EVcouplings Python framework for coevolutionary sequence analysis"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7476-9539","authenticated-orcid":false,"given":"Thomas A","family":"Hopf","sequence":"first","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"},{"name":"Department of Cell Biology, Harvard Medical School, Boston, MA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7548-3682","authenticated-orcid":false,"given":"Anna G","family":"Green","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3412-1102","authenticated-orcid":false,"given":"Benjamin","family":"Schubert","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"},{"name":"Department of Cell Biology, Harvard Medical School, Boston, MA, USA"},{"name":"cBio Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA"}]},{"given":"Sophia","family":"Mersmann","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6689-6423","authenticated-orcid":false,"given":"Charlotta P I","family":"Sch\u00e4rfe","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"},{"name":"Center for Bioinformatics, University of T\u00fcbingen, T\u00fcbingen, Germany"},{"name":"Applied Bioinformatics, Department of Computer Science, T\u00fcbingen, Germany"}]},{"given":"John B","family":"Ingraham","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}]},{"given":"Agnes","family":"Toth-Petroczy","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}]},{"given":"Kelly","family":"Brock","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}]},{"given":"Adam 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