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Open Access Highly Accessed Software

Confab - Systematic generation of diverse low-energy conformers

Noel M O'Boyle12*, Tim Vandermeersch2, Christopher J Flynn1, Anita R Maguire1 and Geoffrey R Hutchison23

Author Affiliations

1 Analytical and Biological Chemistry Research Facility, University College Cork, Western Road, Cork, Co. Cork, Ireland

2 Open Babel development team

3 Department of Chemistry, University of Pittsburgh, Chevron Science Center, 219 Parkman Avenue, Pittsburgh, PA 15260, USA

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Journal of Cheminformatics 2011, 3:8  doi:10.1186/1758-2946-3-8

Published: 16 March 2011

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 webcite.

Graphical abstract