Please use this identifier to cite or link to this item: http://hdl.handle.net/2445/179230
Full metadata record
DC FieldValueLanguage
dc.contributor.authorZivanovic, Sanja-
dc.contributor.authorBayarri, Genís-
dc.contributor.authorColizzi, Francesco-
dc.contributor.authorMoreno, David-
dc.contributor.authorGelpí Buchaca, Josep Lluís-
dc.contributor.authorSoliva, Robert-
dc.contributor.authorHospital Gasch, Adam-
dc.contributor.authorOrozco López, Modesto-
dc.date.accessioned2021-07-20T09:34:40Z-
dc.date.available2021-08-06T05:10:20Z-
dc.date.issued2020-08-06-
dc.identifier.issn1549-9618-
dc.identifier.urihttp://hdl.handle.net/2445/179230-
dc.description.abstractModern high-throughput structure-based drug discovery algorithms consider ligand flexibility, but typically with low accuracy, which results in a loss of performance in the derived models. Here we present the Bioactive Conformational Ensemble (BCE) server and its associated database. The server creates conformational ensembles of drug-like ligands and stores them in the BCE database, where a variety of analyses are offered to the user. The workflow implemented in the BCE server combines enhanced sampling molecular dynamics with self-consistent reaction field quantum mechanics (SCRF/QM) calculations. The server automatizes all the steps to transform 1D or 2D representation of drugs into three dimensional molecules, which are then titrated, parametrized, hydrated and optimized before being subjected to Hamiltonian replica-exchange (HREX) molecular dynamics simulations. Ensembles are collected and subjected to a clustering procedure to derive representative conformers, which are then analyzed at the SCRF/QM level of theory. All structural data is organized in a noSQL database accessible through a graphical interface and in a programmatic manner through a REST API. The server allows the user to define a private workspace and offers a deposition protocol as well as input files for "in house" calculations in those cases where confidentiality is a must. The database and the associated server are available at https://mmb.irbbarcelona.org/BCE-
dc.format.extent12 p.-
dc.format.mimetypeapplication/pdf-
dc.language.isoeng-
dc.publisherAmerican Chemical Society-
dc.relation.isformatofVersió postprint del document publicat a: https://doi.org/10.1021/acs.jctc.0c00305-
dc.relation.ispartofJournal of Chemical Theory and Computation, 2020, vol. 16, num. 10, p. 6586-6597-
dc.relation.urihttps://doi.org/10.1021/acs.jctc.0c00305-
dc.rights(c) American Chemical Society , 2020-
dc.subject.classificationBases de dades-
dc.subject.classificationMolècules-
dc.subject.otherDatabases-
dc.subject.otherMolecules-
dc.titleBioactive conformational ensemble server and database. A public framework to speed up in silico drug discovery.-
dc.typeinfo:eu-repo/semantics/article-
dc.typeinfo:eu-repo/semantics/acceptedVersion-
dc.identifier.idgrec704178-
dc.date.updated2021-07-20T09:34:40Z-
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/H2020/823830/EU//BioExcel-2-
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/H2020/752415/EU//FRAGMENTOME-
dc.rights.accessRightsinfo:eu-repo/semantics/openAccess-
dc.identifier.idimarina6467285-
Appears in Collections:Articles publicats en revistes (Bioquímica i Biomedicina Molecular)
Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))

Files in This Item:
File Description SizeFormat 
704178.pdf2.05 MBAdobe PDFView/Open


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.