{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T16:47:14Z","timestamp":1772556434951,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008667","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,9]],"date-time":"2021-02-09T00:00:00Z","timestamp":1612828800000}}],"reference-count":71,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T00:00:00Z","timestamp":1611792000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Computational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad spectrum of scientific questions in biomedical research. The most accurate methods today are based on homology modelling, i.e. detecting a homologue to the desired target sequence that can be used as a template for modelling. Here we present a versatile open source homology modelling toolbox as foundation for flexible and computationally efficient modelling workflows. ProMod3 is a fully scriptable software platform that can perform all steps required to generate a protein model by homology. Its modular design aims at fast prototyping of novel algorithms and implementing flexible modelling pipelines. Common modelling tasks, such as loop modelling, sidechain modelling or generating a full protein model by homology, are provided as production ready pipelines, forming the starting point for own developments and enhancements. ProMod3 is the central software component of the widely used SWISS-MODEL web-server.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008667","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T19:50:07Z","timestamp":1611863407000},"page":"e1008667","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":253,"title":["ProMod3\u2014A versatile homology modelling toolbox"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0462-1456","authenticated-orcid":true,"given":"Gabriel","family":"Studer","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5921-7007","authenticated-orcid":true,"given":"Gerardo","family":"Tauriello","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9673-9103","authenticated-orcid":true,"given":"Stefan","family":"Bienert","sequence":"additional","affiliation":[]},{"given":"Marco","family":"Biasini","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2257-7508","authenticated-orcid":true,"given":"Niklaus","family":"Johner","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2715-335X","authenticated-orcid":true,"given":"Torsten","family":"Schwede","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2021,1,28]]},"reference":[{"key":"pcbi.1008667.ref001","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1038\/nsb1203-980","article-title":"Announcing the worldwide Protein Data Bank","volume":"10","author":"H Berman","year":"2003","journal-title":"Nat Struct Biol"},{"key":"pcbi.1008667.ref002","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1002\/prot.25800","article-title":"Evaluation of template-based modeling in CASP13","volume":"87","author":"TI Croll","year":"2019","journal-title":"Proteins"},{"key":"pcbi.1008667.ref003","doi-asserted-by":"crossref","first-page":"D313","DOI":"10.1093\/nar\/gkw1132","article-title":"The SWISS-MODEL Repository-new features and functionality","volume":"45","author":"S Bienert","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008667.ref004","doi-asserted-by":"crossref","first-page":"D336","DOI":"10.1093\/nar\/gkt1144","article-title":"ModBase, a database of annotated comparative protein structure models and associated resources","volume":"42","author":"U Pieper","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008667.ref005","doi-asserted-by":"crossref","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: homology modelling of protein structures and complexes","volume":"46","author":"A Waterhouse","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008667.ref006","doi-asserted-by":"crossref","first-page":"2.9.1","DOI":"10.1002\/cpps.20","article-title":"Comparative Protein Structure Modeling Using MODELLER","volume":"86","author":"B Webb","year":"2016","journal-title":"Curr Protoc Protein Sci"},{"key":"pcbi.1008667.ref007","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1016\/j.str.2013.08.005","article-title":"High-resolution comparative modeling with RosettaCM","volume":"21","author":"Y Song","year":"2013","journal-title":"Structure"},{"key":"pcbi.1008667.ref008","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER Suite: protein structure and function prediction","volume":"12","author":"J Yang","year":"2015","journal-title":"Nat Methods"},{"key":"pcbi.1008667.ref009","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1002\/prot.22488","article-title":"Improved prediction of protein side-chain conformations with SCWRL4","author":"GG Krivov","year":"2009","journal-title":"Proteins: Structure, Function. 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