Abstract
The development of an energy or scoring function for protein structure prediction is greatly enhanced by testing the function on a set of computer-generated conformations (decoys) to determine whether it can readily distinguish native-like conformations from nonnative ones. We have created "Decoys 'R' Us," a database containing many such sets of conformations, to provide a resource that allows scoring functions to be improved.
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Selected References
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- Holm L., Sander C. Evaluation of protein models by atomic solvation preference. J Mol Biol. 1992 May 5;225(1):93–105. doi: 10.1016/0022-2836(92)91028-n. [DOI] [PubMed] [Google Scholar]
- Huang E. S., Subbiah S., Tsai J., Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J Mol Biol. 1996 Apr 5;257(3):716–725. doi: 10.1006/jmbi.1996.0196. [DOI] [PubMed] [Google Scholar]
- Lazaridis T., Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol. 1999 May 7;288(3):477–487. doi: 10.1006/jmbi.1999.2685. [DOI] [PubMed] [Google Scholar]
- Novotný J., Bruccoleri R., Karplus M. An analysis of incorrectly folded protein models. Implications for structure predictions. J Mol Biol. 1984 Aug 25;177(4):787–818. doi: 10.1016/0022-2836(84)90049-4. [DOI] [PubMed] [Google Scholar]
- Park B. H., Huang E. S., Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol. 1997 Mar 7;266(4):831–846. doi: 10.1006/jmbi.1996.0809. [DOI] [PubMed] [Google Scholar]
- Park B., Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol. 1996 May 3;258(2):367–392. doi: 10.1006/jmbi.1996.0256. [DOI] [PubMed] [Google Scholar]
- Samudrala R., Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol. 1998 Feb 6;275(5):895–916. doi: 10.1006/jmbi.1997.1479. [DOI] [PubMed] [Google Scholar]
- Samudrala R., Xia Y., Huang E., Levitt M. Ab initio protein structure prediction using a combined hierarchical approach. Proteins. 1999;Suppl 3:194–198. doi: 10.1002/(sici)1097-0134(1999)37:3+<194::aid-prot24>3.3.co;2-6. [DOI] [PubMed] [Google Scholar]
- Simons K. T., Bonneau R., Ruczinski I., Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins. 1999;Suppl 3:171–176. doi: 10.1002/(sici)1097-0134(1999)37:3+<171::aid-prot21>3.3.co;2-q. [DOI] [PubMed] [Google Scholar]
- Simons K. T., Ruczinski I., Kooperberg C., Fox B. A., Bystroff C., Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 1999 Jan 1;34(1):82–95. doi: 10.1002/(sici)1097-0134(19990101)34:1<82::aid-prot7>3.0.co;2-a. [DOI] [PubMed] [Google Scholar]
- Wang Y., Zhang H., Li W., Scott R. A. Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci U S A. 1995 Jan 31;92(3):709–713. doi: 10.1073/pnas.92.3.709. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wei L., Huang E. S., Altman R. B. Are predicted structures good enough to preserve functional sites? Structure. 1999 Jun 15;7(6):643–650. doi: 10.1016/s0969-2126(99)80085-9. [DOI] [PubMed] [Google Scholar]