{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T17:54:21Z","timestamp":1732038861373},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,11]],"date-time":"2020-01-11T00:00:00Z","timestamp":1578700800000},"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\/501100002850","name":"Fondo Nacional de Desarrollo Cientifico y Tecnologico","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002850","name":"FONDECYT","doi-asserted-by":"publisher","award":["1170662","1170718","CONICYT-FONDEQUIP-EQM160063"],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Root mean square deviation (RMSD) is one of the most useful and straightforward features for structural comparison between different conformations of the same molecule. Commonly, protein-ligand docking programs have included some utilities that allow the calculation of this value; however, they only work efficiently when exists a complete atom label equivalence between the evaluated conformations.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We present LigRMSD, a free web-server for the automatic matching and RMSD calculations among identical or similar chemical compounds. This server allows the user to submit only a pair of identical or similar molecules or dataset of similar compounds to compare their three-dimensional conformations.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n LigRMSD can be freely accessed at https:\/\/ligrmsd.appsbio.utalca.cl.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa018","type":"journal-article","created":{"date-parts":[[2020,1,7]],"date-time":"2020-01-07T20:11:43Z","timestamp":1578427903000},"page":"2912-2914","source":"Crossref","is-referenced-by-count":102,"title":["LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking"],"prefix":"10.1093","volume":"36","author":[{"given":"Jos\u00e9 Luis","family":"Vel\u00e1zquez-Libera","sequence":"first","affiliation":[{"name":"Center for Bioinformatics, Simulations and Modelling , , Talca 3460000, Chile"},{"name":"Universidad de Talca , , Talca 3460000, Chile"}]},{"given":"Fabio","family":"Dur\u00e1n-Verdugo","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Simulations and Modelling , , Talca 3460000, Chile"},{"name":"Universidad de Talca , , Talca 3460000, Chile"}]},{"given":"Alejandro","family":"Vald\u00e9s-Jim\u00e9nez","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Simulations and Modelling , , Talca 3460000, Chile"},{"name":"Universidad de Talca , , Talca 3460000, Chile"},{"name":"Computer Architecture Department, Universitat Polit\u00e9cnica de Catalunya , Barcelona 08034, Spain"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-2858-1789","authenticated-orcid":false,"given":"Gabriel","family":"N\u00fa\u00f1ez-Vivanco","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Simulations and Modelling , , Talca 3460000, Chile"},{"name":"Universidad de Talca , , Talca 3460000, Chile"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-0182-1444","authenticated-orcid":false,"given":"Julio","family":"Caballero","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Simulations and Modelling , , Talca 3460000, Chile"},{"name":"Universidad de Talca , , Talca 3460000, Chile"}]}],"member":"286","published-online":{"date-parts":[[2020,1,11]]},"reference":[{"key":"2023013111482065000_btaa018-B1","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","article-title":"GROMACS: a message-passing parallel molecular dynamics implementation","volume":"9","author":"Berendsen","year":"1995","journal-title":"Comput. 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