Confab - Systematic generation of diverse low-energy conformers
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 conf...
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Veröffentlicht in: | Journal of cheminformatics 2011-03, Vol.3 (1), p.8-8, Article 8 |
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Format: | Artikel |
Sprache: | eng |
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Zusammenfassung: | 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
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ISSN: | 1758-2946 1758-2946 |
DOI: | 10.1186/1758-2946-3-8 |