Journal
JOURNAL OF CHEMINFORMATICS
Volume 3, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/1758-2946-3-8
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Funding
- Health Research Board [PD/2009/13]
- Health Research Board (HRB) [PD-2009-13] Funding Source: Health Research Board (HRB)
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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 angstrom at a diversity level of 1.5 angstrom and an energy cutoff of 50 kcal/mol. Conclusions: Confab is available from http://confab.googlecode.com.
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