title: Confab - Systematic generation of diverse low-energy conformers.
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.
authors.affiliation: Analytical and Biological Chemistry Research Facility, University College Cork, Western Road, Cork, Co, Cork, Ireland. baoilleach@gmail.com.
authors.forename: Noel M
authors.initials: NM
authors.lastname: O'Boyle
authors.forename: Tim
authors.initials: T
authors.lastname: Vandermeersch
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Flynn
authors.forename: Anita R
authors.initials: AR
authors.lastname: Maguire
authors.forename: Geoffrey R
authors.initials: GR
authors.lastname: Hutchison