Confab - Systematic generation of diverse low-energy conformers

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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 at a diversity level of 1.5 and an energy cutoff of 50 kcal/mol. Conclusions: Confab is available from http://confab.googlecode.com. © 2011 O'Boyle et al; licensee Chemistry Central Ltd.

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O’Boyle, N. M., Vandermeersch, T., Flynn, C. J., Maguire, A. R., & Hutchison, G. R. (2011). Confab - Systematic generation of diverse low-energy conformers. Journal of Cheminformatics, 3(1). https://doi.org/10.1186/1758-2946-3-8

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