{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T20:03:29Z","timestamp":1762113809586,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,2,27]],"date-time":"2020-02-27T00:00:00Z","timestamp":1582761600000},"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\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"CAPES","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CAPES\/Drug Discovery","award":["23038.007777\/2014-87"],"award-info":[{"award-number":["23038.007777\/2014-87"]}]},{"name":"CAPES\/PROBRAL","award":["88881.198766\/2018-01"],"award-info":[{"award-number":["88881.198766\/2018-01"]}]},{"DOI":"10.13039\/501100004263","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado do Rio Grande do Sul","doi-asserted-by":"publisher","award":["16\/2551-0000520-6"],"award-info":[{"award-number":["16\/2551-0000520-6"]}],"id":[{"id":"10.13039\/501100004263","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005156","name":"Alexander von Humboldt-Stiftung","doi-asserted-by":"publisher","award":["BRA 1190826 HFST"],"award-info":[{"award-number":["BRA 1190826 HFST"]}],"id":[{"id":"10.13039\/100005156","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The conformational space of small molecules can be vast and difficult to assess. Molecular dynamics (MD) simulations of free ligands in solution have been applied to predict conformational populations, but their characterization is often based on clustering algorithms or manual efforts.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we introduce ConfID, an analytical tool for conformational characterization of small molecules using MD trajectories. The evolution of conformational sampling and population frequencies throughout trajectories is calculated to check for sampling convergence while allowing to map relevant conformational transitions. The tool is designed to track conformational transition events and calculate time-dependent properties for each conformational population detected.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Toolkit and documentation are freely available at http:\/\/sbcb.inf.ufrgs.br\/confid<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>marcelo.poleto@ufv.br or bigrisci@inf.ufrgs.br<\/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\/btaa130","type":"journal-article","created":{"date-parts":[[2020,2,24]],"date-time":"2020-02-24T20:16:57Z","timestamp":1582575417000},"page":"3576-3577","source":"Crossref","is-referenced-by-count":3,"title":["<i>ConfID<\/i>: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories"],"prefix":"10.1093","volume":"36","author":[{"given":"Marcelo D","family":"Pol\u00eato","sequence":"first","affiliation":[{"name":"Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900"},{"name":"Departamento de Biologia Geral , Universidade Federal de Vi\u00e7osa, Vi\u00e7osa 36570-000"}]},{"given":"Bruno I","family":"Grisci","sequence":"additional","affiliation":[{"name":"Instituto de Inform\u00e1tica , Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Brazil"}]},{"given":"Marcio","family":"Dorn","sequence":"additional","affiliation":[{"name":"Instituto de Inform\u00e1tica , Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Brazil"}]},{"given":"Hugo","family":"Verli","sequence":"additional","affiliation":[{"name":"Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900"}]}],"member":"286","published-online":{"date-parts":[[2020,2,27]]},"reference":[{"key":"2023062312021230700_btaa130-B1","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1021\/acs.jpcb.8b10139","article-title":"Development of GROMOS-compatible parameter set for simulations of chalcones and flavonoids","volume":"123","author":"Arantes","year":"2019","journal-title":"J. Phys. Chem. B"},{"key":"2023062312021230700_btaa130-B2","doi-asserted-by":"crossref","first-page":"2218","DOI":"10.1021\/acs.jcim.9b00171","article-title":"Conformational properties of the chemotherapeutic drug analogue epothilone a: how to model a flexible protein ligand using scarcely available experimental data","volume":"59","author":"Dolenc","year":"2019","journal-title":"J. Chem. Inf. Model"},{"key":"2023062312021230700_btaa130-B3","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1021\/ml500220a","article-title":"Protein-ligand cocrystal structures: we can do better","volume":"5","author":"Reynolds","year":"2014","journal-title":"ACS Med. Chem. Lett"},{"key":"2023062312021230700_btaa130-B4","doi-asserted-by":"crossref","first-page":"2562","DOI":"10.1021\/acs.jcim.5b00654","article-title":"Better informed distance geometry: using what we know to improve conformation generation","volume":"55","author":"Riniker","year":"2015","journal-title":"J. Chem. Inf. Model"},{"key":"2023062312021230700_btaa130-B5","doi-asserted-by":"crossref","first-page":"3214","DOI":"10.1021\/jm049216s","article-title":"DASH: a novel analysis method for molecular dynamics simulation data. Analysis of ligands of PPAR-\u03b3","volume":"9","author":"Salt","year":"2005","journal-title":"J. Med. Chem"},{"key":"2023062312021230700_btaa130-B6","doi-asserted-by":"crossref","first-page":"4670","DOI":"10.1002\/jps.21378","article-title":"High-field solution NMR spectroscopy as a tool for assessing protein interactions with small molecule ligands","volume":"97","author":"Skinner","year":"2008","journal-title":"J. Pharm. Sci"},{"key":"2023062312021230700_btaa130-B7","doi-asserted-by":"crossref","first-page":"2338","DOI":"10.1021\/acs.jcim.5b00243","article-title":"First-principles molecular structure search with a genetic algorithm","volume":"55","author":"Supady","year":"2015","journal-title":"J. Chem. Inf. Model"},{"key":"2023062312021230700_btaa130-B8","doi-asserted-by":"crossref","first-page":"9970","DOI":"10.1002\/anie.201804917","article-title":"An unusual intramolecular halogen bond guides conformational selection","volume":"57","author":"Tesch","year":"2018","journal-title":"Angew. Chem. Int. Ed"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa130\/32923760\/btaa130.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/11\/3576\/50670787\/bioinformatics_36_11_3576.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/11\/3576\/50670787\/bioinformatics_36_11_3576.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,23]],"date-time":"2023-06-23T12:03:35Z","timestamp":1687521815000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/11\/3576\/5762609"}},"subtitle":[],"editor":[{"given":"Yann","family":"Ponty","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,2,27]]},"references-count":8,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2020,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa130","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,6]]},"published":{"date-parts":[[2020,2,27]]}}}