The DOI matches its Crossref record; 20 of the 20 references it cites were found in a registry or an index.
Confab - Systematic generation of diverse low-energy conformers
Open accessAbstract
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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Cites
Open Babel: An open chemical toolbox
O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011) · Journal of Cheminformatics · doi:10.1186/1758-2946-3-33 · Cited by 10,939
Self-citationMerck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
Halgren, T. A. (1996) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-p · Cited by 5,306
A new force field for molecular mechanical simulation of nucleic acids and proteins
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An all atom force field for simulations of proteins and nucleic acids
Weiner, S. J., Kollman, P. A., Nguyen, D. T., & Case, D. A. (1986) · Journal of Computational Chemistry · doi:10.1002/jcc.540070216 · Cited by 3,437
A solution for the best rotation to relate two sets of vectors
Kabsch, W. (1976) · Acta Crystallographica Section A · doi:10.1107/s0567739476001873 · Cited by 3,187
Hawkins, P. C. D., Skillman, A. G., Warren, G. L., Ellingson, B. A., & Stahl, M. T. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci100031x · Cited by 1,607
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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers
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Cited by
Open Babel: An open chemical toolbox
O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011) · Journal of Cheminformatics · doi:10.1186/1758-2946-3-33 · Cited by 10,939
Self-citationKozakov, D., Grove, L. E., Hall, D. R., Bohnuud, T., Mottarella, S. E., Luo, L., Xia, B., Beglov, D., & Vajda, S. (2015) · Nature Protocols · doi:10.1038/nprot.2015.043 · Cited by 648
Metadata
- Authors
- O'Boyle, N. M., Vandermeersch, T., Flynn, C. J., Maguire, A. R., & Hutchison, G. R.
- Venue
- Journal of Cheminformatics
- Published
- 2011-03-16
- Volume
- 3
- Issue
- 1
- Pages
- 8-8
- ISSN
- 1758-2946 (ISSN-L)
- OpenAlex
- W2127463492
- Cited by
- 305
- References
- 20
- FWCI
- 5.38
- Type
- journal article
- Language
- en
- Open access
- gold
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