Confab - Systematic generation of diverse low-energy conformers
O'Boyle, Noel M.
Flynn, Christopher J.
Maguire, Anita R.
Hutchison, Geoffrey R.
Chemistry Central Ltd.
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
Low energy conformers , Confab
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