Confab - Systematic generation of diverse low-energy conformers

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dc.contributor.authorO'Boyle, Noel M.
dc.contributor.authorVandermeersch, Tim
dc.contributor.authorFlynn, Christopher J.
dc.contributor.authorMaguire, Anita R.
dc.contributor.authorHutchison, Geoffrey R.
dc.contributor.funderHealth Research Boarden
dc.date.accessioned2011-04-14T16:22:57Z
dc.date.available2011-04-14T16:22:57Z
dc.date.copyright2010
dc.date.issued2011-03-16
dc.description.abstractBackground: Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion. Results: Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD) relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 Å at a diversity level of 1.5 Å and an energy cutoff of 50 kcal/mol. Conclusions: Confab is available from http://confab.googlecode.comen
dc.description.sponsorshipHealth Research Board (Career Development Fellowship, PD/2009/13)en
dc.description.statusPeer revieweden
dc.description.urihttp://confab.googlecode.comen
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationO'Boyle NM, Vandermeersch T, Flynn CJ, Maguire AR, Hutchison GR (2011) 'Confab - Systematic generation of diverse low-energy conformers'. Journal of Cheminformatics, 3:8en
dc.identifier.doi10.1186/1758-2946-3-8
dc.identifier.issn1758-2946
dc.identifier.issued8en
dc.identifier.journaltitleJournal of Cheminformaticsen
dc.identifier.urihttps://hdl.handle.net/10468/288
dc.identifier.volume3en
dc.language.isoenen
dc.publisherChemistry Central Ltd.en
dc.relation.urihttp://www.jcheminf.com/content/3/1/8
dc.rights© 2011 O’Boyle et al; licensee Chemistry Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/en
dc.subjectLow energy conformersen
dc.subjectConfaben
dc.subject.lcshStereochemistry--Data processingen
dc.subject.lcshStereochemistry--Computer simulationen
dc.subject.lcshConformational analysisen
dc.titleConfab - Systematic generation of diverse low-energy conformersen
dc.typeArticle (peer-reviewed)en
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