Confab: Systematic generation of diverse low-energy conformers

Noel M. O’Boyle, Tim Vandermeersch, Christopher J. Flynn, Anita R. Maguire, Geoffrey R. Hutchison. “Confab: Systematic generation of diverse low-energy conformers” J. Cheminf. 2011 3:8. DOI

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

Note: Confab is now integrated directly into Open Babel v2.4 and later