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 A at a diversity level of 1.5 A and an energy cutoff of 50 kcal/mol.CONCLUSIONS:Confab is available from http://confab.googlecode.com webcite.
%0 Journal Article
%1 OBoyle2011
%A O'Boyle, Noel M.
%A Vandermeersch, Tim
%A Flynn, Christopher J.
%A Maguire, Anita R.
%A Hutchison, Geoffrey R.
%D 2011
%J Journal of Cheminformatics
%K algorithms conflab conformation openbabel opensource rotatable\_bonds
%N 1
%P 8+
%R 10.1186/1758-2946-3-8
%T Confab - Systematic generation of diverse low-energy conformers
%U http://dx.doi.org/10.1186/1758-2946-3-8
%V 3
%X 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 A at a diversity level of 1.5 A and an energy cutoff of 50 kcal/mol.CONCLUSIONS:Confab is available from http://confab.googlecode.com webcite.
@article{OBoyle2011,
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 A at a diversity level of 1.5 A and an energy cutoff of 50 kcal/mol.CONCLUSIONS:Confab is available from http://confab.googlecode.com webcite.}},
added-at = {2019-03-11T21:00:05.000+0100},
author = {O'Boyle, Noel M. and Vandermeersch, Tim and Flynn, Christopher J. and Maguire, Anita R. and Hutchison, Geoffrey R.},
biburl = {https://www.bibsonomy.org/bibtex/203da3a6ce28cf0024b188d11cbc9008c/fairybasslet},
citeulike-article-id = {9004566},
citeulike-linkout-0 = {http://dx.doi.org/10.1186/1758-2946-3-8},
citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/21410983},
citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=21410983},
doi = {10.1186/1758-2946-3-8},
interhash = {ae441d0216c08f27246f27e7582330d6},
intrahash = {03da3a6ce28cf0024b188d11cbc9008c},
issn = {1758-2946},
journal = {Journal of Cheminformatics},
keywords = {algorithms conflab conformation openbabel opensource rotatable\_bonds},
number = 1,
pages = {8+},
pmid = {21410983},
posted-at = {2013-11-15 04:03:27},
priority = {2},
timestamp = {2019-03-11T21:06:37.000+0100},
title = {{Confab - Systematic generation of diverse low-energy conformers}},
url = {http://dx.doi.org/10.1186/1758-2946-3-8},
volume = 3,
year = 2011
}