{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T06:45:35Z","timestamp":1781678735584,"version":"3.54.5"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,2,2]],"date-time":"2024-02-02T00:00:00Z","timestamp":1706832000000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["2020\/39\/B\/NZ2\/01301"],"award-info":[{"award-number":["2020\/39\/B\/NZ2\/01301"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["2019\/33\/B\/NZ2\/02100"],"award-info":[{"award-number":["2019\/33\/B\/NZ2\/02100"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The structural modeling of peptides can be a useful aid in the discovery of new drugs and a deeper understanding of the molecular mechanisms of life. Here we present a novel multiscale protocol for the structure prediction of linear and cyclic peptides. The protocol combines two main stages: coarse-grained simulations using the CABS-flex standalone package and an all-atom reconstruction-optimization process using the Modeller program. We evaluated the protocol on a set of linear peptides and two sets of cyclic peptides, with cyclization through the backbone and disulfide bonds. A comparison with other state-of-the-art tools (APPTEST, PEP-FOLD, ESMFold and AlphaFold implementation in ColabFold) shows that for most cases, AlphaFold offers the highest resolution. However, CABS-flex is competitive, particularly when it comes to short linear peptides. As demonstrated, the protocol performance can be further improved by combination with the residue\u2013residue contact prediction method or more efficient scoring. The protocol is included in the CABS-flex standalone package along with online documentation to aid users in predicting the structure of peptides and mini-proteins.<\/jats:p>","DOI":"10.1093\/bib\/bbae003","type":"journal-article","created":{"date-parts":[[2024,2,2]],"date-time":"2024-02-02T12:22:35Z","timestamp":1706876555000},"source":"Crossref","is-referenced-by-count":15,"title":["Structure prediction of linear and cyclic peptides using CABS-flex"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1832-4364","authenticated-orcid":false,"given":"Aleksandra","family":"Badaczewska-Dawid","sequence":"first","affiliation":[{"name":"Genome Informatics Facility , Office of Biotechnology, , Ames, 50011 IA,","place":["USA"]},{"name":"Iowa State University , Office of Biotechnology, , Ames, 50011 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Warsaw,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7623-0935","authenticated-orcid":false,"given":"Sebastian","family":"Kmiecik","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Center , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","place":["Poland"]},{"name":"University of Warsaw , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,2,1]]},"reference":[{"key":"2024111603064226200_ref1","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1021\/acs.jmedchem.7b00318","article-title":"The current state of peptide drug discovery: back to the future?","volume":"61","author":"Henninot","year":"2018","journal-title":"J Med 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