{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:06Z","timestamp":1772138046145,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,7,8]],"date-time":"2021-07-08T00:00:00Z","timestamp":1625702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["VR-NT 2016-03798"],"award-info":[{"award-number":["VR-NT 2016-03798"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"name":"SNIC"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Contact predictions within a protein have recently become a viable method for accurate prediction of protein structure. Using predicted distance distributions has been shown in many cases to be superior to only using a binary contact annotation. Using predicted interprotein distances has also been shown to be able to dock some protein dimers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present pyconsFold. Using CNS as its underlying folding mechanism and predicted contact distance it outperforms regular contact prediction-based modeling on our dataset of 210 proteins. It performs marginally worse than the state-of-the-art pyRosetta folding pipeline but is on average about 20 times faster per model. More importantly pyconsFold can also be used as a fold-and-dock protocol by using predicted interprotein contacts\/distances to simultaneously fold and dock two protein chains.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>pyconsFold is implemented in Python 3 with a strong focus on using as few dependencies as possible for longevity. It is available both as a pip package in Python 3 and as source code on GitHub and is published under the GPLv3 license. The data underlying this article together with source code are available on github, at https:\/\/github.com\/johnlamb\/pyconsfold.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab353","type":"journal-article","created":{"date-parts":[[2021,5,6]],"date-time":"2021-05-06T09:39:37Z","timestamp":1620293977000},"page":"3959-3960","source":"Crossref","is-referenced-by-count":8,"title":["pyconsFold: a fast and easy tool for modeling and docking using distance predictions"],"prefix":"10.1093","volume":"37","author":[{"given":"J","family":"Lamb","sequence":"first","affiliation":[{"name":"Science for Life Laboratory, Stockholm University , Solna SE-171 21, Sweden"},{"name":"Department of Biochemistry and Biophysics, Stockholm University , Stockholm SE-106 91, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7115-9751","authenticated-orcid":false,"given":"A","family":"Elofsson","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Stockholm University , Solna SE-171 21, Sweden"},{"name":"Department of Biochemistry and Biophysics, Stockholm University , Stockholm SE-106 91, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2021,7,8]]},"reference":[{"key":"2023051607344131200_btab353-B1","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1002\/prot.24829","article-title":"CONFOLD: residue\u2013residue contact-guided ab initio protein folding","volume":"83","author":"Adhikari","year":"2015","journal-title":"Proteins"},{"key":"2023051607344131200_btab353-B2","doi-asserted-by":"crossref","first-page":"e0161879","DOI":"10.1371\/journal.pone.0161879","article-title":"Dockq: a quality measure for protein-protein docking models","volume":"11","author":"Basu","year":"2016","journal-title":"PLoS One"},{"key":"2023051607344131200_btab353-B3","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":"Brunger","year":"2007","journal-title":"Nat. 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