{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T12:01:21Z","timestamp":1774267281804,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,11,23]],"date-time":"2020-11-23T00:00:00Z","timestamp":1606089600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Associazione Italiana Ricerca sul Cancro","doi-asserted-by":"crossref","award":["20447"],"award-info":[{"award-number":["20447"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The PyMod project is designed to act as a fully integrated interface between the popular molecular graphics viewer PyMOL, and some of the most frequently used tools for structural bioinformatics, e.g. BLAST, HMMER, Clustal, MUSCLE, PSIPRED, DOPE and MODELLER. Here we report its latest release, PyMod 3, which has been completely renewed with a graphical interface written in PyQt, to make it compatible with the most recent PyMOL versions, and has been extended with a large set of new functionalities compared to its predecessor, i.e. PyMod 2. Starting from the amino acid sequence of a target protein, users can take advantage of PyMod 3 to carry out all the steps of the homology modeling process (i.e. template searching, target\u2013template sequence alignment, model building and quality assessment). Additionally, the integrated tools in PyMod 3 may also be used alone, in order to extend PyMOL with a wide range of capabilities. Sequence similarity searches, multiple sequence\/structure alignment building, phylogenetic trees and evolutionary conservation analyses, domain parsing, single\/multiple chains and loop modeling can be performed in the PyMod 3\/PyMOL environment.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>A cross-platform PyMod 3 installer package for Windows, Linux and Mac OS X and a complete user guide with tutorials, are available at https:\/\/github.com\/pymodproject\/pymod<\/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\/btaa849","type":"journal-article","created":{"date-parts":[[2020,9,17]],"date-time":"2020-09-17T13:45:18Z","timestamp":1600350318000},"page":"1471-1472","source":"Crossref","is-referenced-by-count":138,"title":["PyMod 3: a complete suite for structural bioinformatics in PyMOL"],"prefix":"10.1093","volume":"37","author":[{"given":"Giacomo","family":"Janson","sequence":"first","affiliation":[{"name":"Sapienza Universit\u00e0 di Roma Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, , 00185 Rome, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9078-7545","authenticated-orcid":false,"given":"Alessandro","family":"Paiardini","sequence":"additional","affiliation":[{"name":"Sapienza Universit\u00e0 di Roma Department of Biochemical Sciences \u201cA. Rossi Fanelli\u201d, , 00185 Rome, Italy"}]}],"member":"286","published-online":{"date-parts":[[2020,11,23]]},"reference":[{"key":"2023051709341891800_btaa849-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023051709341891800_btaa849-B2","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-13-S4-S2","article-title":"PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL","volume":"13","author":"Bramucci","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023051709341891800_btaa849-B3","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051709341891800_btaa849-B4","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"2023051709341891800_btaa849-B5","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023051709341891800_btaa849-B6","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023051709341891800_btaa849-B7","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1093\/bioinformatics\/btw638","article-title":"PyMod 2.0: improvements in protein sequence\u2013structure analysis and homology modeling within PyMOL","volume":"33","author":"Janson","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051709341891800_btaa849-B8","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","article-title":"Protein secondary structure prediction based on position-specific scoring matrices","volume":"292","author":"Jones","year":"1999","journal-title":"J. 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