%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 }