Confab - Systematic generation of diverse low-energy conformers

Show simple item record

dc.contributor.author O'Boyle, Noel M.
dc.contributor.author Vandermeersch, Tim
dc.contributor.author Flynn, Christopher J.
dc.contributor.author Maguire, Anita R.
dc.contributor.author Hutchison, Geoffrey R.
dc.date.accessioned 2011-04-14T16:22:57Z
dc.date.available 2011-04-14T16:22:57Z
dc.date.copyright 2010
dc.date.issued 2011-03-16
dc.identifier.citation O'Boyle NM, Vandermeersch T, Flynn CJ, Maguire AR, Hutchison GR (2011) 'Confab - Systematic generation of diverse low-energy conformers'. Journal of Cheminformatics, 3:8 en
dc.identifier.volume 3 en
dc.identifier.issued 8 en
dc.identifier.issn 1758-2946
dc.identifier.uri http://hdl.handle.net/10468/288
dc.identifier.doi 10.1186/1758-2946-3-8
dc.description.abstract Background: 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.com en
dc.description.sponsorship Health Research Board (Career Development Fellowship, PD/2009/13) en
dc.description.uri http://confab.googlecode.com en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Chemistry Central Ltd. en
dc.relation.uri http://www.jcheminf.com/content/3/1/8
dc.rights © 2011 O’Boyle et al; licensee Chemistry Central Ltd. en
dc.rights.uri http://creativecommons.org/licenses/by/3.0/ en
dc.subject Low energy conformers en
dc.subject Confab en
dc.subject.lcsh Stereochemistry--Data processing en
dc.subject.lcsh Stereochemistry--Computer simulation en
dc.subject.lcsh Conformational analysis en
dc.title Confab - Systematic generation of diverse low-energy conformers en
dc.type Article (peer-reviewed) en
dc.internal.authorurl http://publish.ucc.ie/researchprofiles/C019/noboyle en
dc.internal.authorurl http://publish.ucc.ie/researchprofiles/V001/amaguire en
dc.internal.authorcontactother Noel O'Boyle, School Of Pharmacy, University College Cork, Cork, Ireland. Tel: +353-21-490-3000 Email: n.oboyle@ucc.ie en
dc.internal.authorcontactother Christopher J. Flynn, Analytical and Biological Chemistry Research Facility, University College Cork, Western Road, Cork, Ireland. +353-21-490-3000 en
dc.internal.authorcontactother Anita R. Maguire, Vice President For Research & Innovation, Office of The Vp For Research & Innovation, Food Science Building, Block E, University College Cork, College Road, Cork, Ireland. Tel: +353-21-490-3000 Email: a.maguire@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.rssid 76416121
dc.internal.pmid 21410983
dc.contributor.funder Health Research Board en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Journal of Cheminformatics en
dc.internal.copyrightchecked RoMEO en
dc.internal.IRISemailaddress n.oboyle@ucc.ie en


Files in this item

The following license files are associated with this item:

This item appears in the following Collection(s)

Show simple item record

© 2011 O’Boyle et al; licensee Chemistry Central Ltd. Except where otherwise noted, this item's license is described as © 2011 O’Boyle et al; licensee Chemistry Central Ltd.
This website uses cookies. By using this website, you consent to the use of cookies in accordance with the UCC Privacy and Cookies Statement. For more information about cookies and how you can disable them, visit our Privacy and Cookies statement