Confab - Systematic generation of diverse low-energy conformers
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-03-01
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| Series: | Journal of Cheminformatics |
| Online Access: | http://www.jcheminf.com/content/3/1/8 |
| _version_ | 1818751147480973312 |
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| author | O'Boyle Noel M Vandermeersch Tim Flynn Christopher J Maguire Anita R Hutchison Geoffrey R |
| author_facet | O'Boyle Noel M Vandermeersch Tim Flynn Christopher J Maguire Anita R Hutchison Geoffrey R |
| author_sort | O'Boyle Noel M |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>Confab is available from <url>http://confab.googlecode.com</url>.</p> |
| first_indexed | 2024-12-18T04:30:57Z |
| format | Article |
| id | doaj.art-a85540df5c2f44b49c3abd2f160c2bea |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-18T04:30:57Z |
| publishDate | 2011-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-a85540df5c2f44b49c3abd2f160c2bea2022-12-21T21:20:59ZengBMCJournal of Cheminformatics1758-29462011-03-0131810.1186/1758-2946-3-8Confab - Systematic generation of diverse low-energy conformersO'Boyle Noel MVandermeersch TimFlynn Christopher JMaguire Anita RHutchison Geoffrey R<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>Confab is available from <url>http://confab.googlecode.com</url>.</p>http://www.jcheminf.com/content/3/1/8 |
| spellingShingle | O'Boyle Noel M Vandermeersch Tim Flynn Christopher J Maguire Anita R Hutchison Geoffrey R Confab - Systematic generation of diverse low-energy conformers Journal of Cheminformatics |
| title | Confab - Systematic generation of diverse low-energy conformers |
| title_full | Confab - Systematic generation of diverse low-energy conformers |
| title_fullStr | Confab - Systematic generation of diverse low-energy conformers |
| title_full_unstemmed | Confab - Systematic generation of diverse low-energy conformers |
| title_short | Confab - Systematic generation of diverse low-energy conformers |
| title_sort | confab systematic generation of diverse low energy conformers |
| url | http://www.jcheminf.com/content/3/1/8 |
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