Abstract
We present a fast method for finding optimal parameters for a low-resolution (threading) force field intended to distinguish correct from incorrect folds for a given protein sequence. In contrast to other methods, the parameterization uses information from >10(7) misfolded structures as well as a set of native sequence-structure pairs. In addition to testing the resulting force field's performance on the protein sequence threading problem, results are shown that characterize the number of parameters necessary for effective structure recognition.
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- Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164–170. doi: 10.1126/science.1853201. [DOI] [PubMed] [Google Scholar]
- Bryngelson J. D., Onuchic J. N., Socci N. D., Wolynes P. G. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 1995 Mar;21(3):167–195. doi: 10.1002/prot.340210302. [DOI] [PubMed] [Google Scholar]
- Defay T. R., Cohen F. E. Multiple sequence information for threading algorithms. J Mol Biol. 1996 Sep 20;262(2):314–323. doi: 10.1006/jmbi.1996.0515. [DOI] [PubMed] [Google Scholar]
- Hao M. H., Scheraga H. A. How optimization of potential functions affects protein folding. Proc Natl Acad Sci U S A. 1996 May 14;93(10):4984–4989. doi: 10.1073/pnas.93.10.4984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hendlich M., Lackner P., Weitckus S., Floeckner H., Froschauer R., Gottsbacher K., Casari G., Sippl M. J. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol. 1990 Nov 5;216(1):167–180. doi: 10.1016/S0022-2836(05)80068-3. [DOI] [PubMed] [Google Scholar]
- Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 1994 Mar;3(3):522–524. doi: 10.1002/pro.5560030317. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jones D. T., Thornton J. M. Potential energy functions for threading. Curr Opin Struct Biol. 1996 Apr;6(2):210–216. doi: 10.1016/s0959-440x(96)80076-5. [DOI] [PubMed] [Google Scholar]
- Jones D., Thornton J. Protein fold recognition. J Comput Aided Mol Des. 1993 Aug;7(4):439–456. doi: 10.1007/BF02337560. [DOI] [PubMed] [Google Scholar]
- Kirkpatrick S., Gelatt C. D., Jr, Vecchi M. P. Optimization by simulated annealing. Science. 1983 May 13;220(4598):671–680. doi: 10.1126/science.220.4598.671. [DOI] [PubMed] [Google Scholar]
- Koretke K. K., Luthey-Schulten Z., Wolynes P. G. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Protein Sci. 1996 Jun;5(6):1043–1059. doi: 10.1002/pro.5560050607. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol. 1976 Jun 14;104(1):59–107. doi: 10.1016/0022-2836(76)90004-8. [DOI] [PubMed] [Google Scholar]
- Maiorov V. N., Crippen G. M. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol. 1992 Oct 5;227(3):876–888. doi: 10.1016/0022-2836(92)90228-c. [DOI] [PubMed] [Google Scholar]
- Mirny L. A., Shakhnovich E. I. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol. 1996 Dec 20;264(5):1164–1179. doi: 10.1006/jmbi.1996.0704. [DOI] [PubMed] [Google Scholar]
- Onuchic J. N., Wolynes P. G., Luthey-Schulten Z., Socci N. D. Toward an outline of the topography of a realistic protein-folding funnel. Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3626–3630. doi: 10.1073/pnas.92.8.3626. [DOI] [PMC free article] [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]
- Shakhnovich E. I., Gutin A. M. Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach. Biophys Chem. 1989 Nov;34(3):187–199. doi: 10.1016/0301-4622(89)80058-4. [DOI] [PubMed] [Google Scholar]
- Sippl M. J. Knowledge-based potentials for proteins. Curr Opin Struct Biol. 1995 Apr;5(2):229–235. doi: 10.1016/0959-440x(95)80081-6. [DOI] [PubMed] [Google Scholar]
- Sun S., Thomas P. D., Dill K. A. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng. 1995 Aug;8(8):769–778. doi: 10.1093/protein/8.8.769. [DOI] [PubMed] [Google Scholar]
- Tanaka S., Scheraga H. A. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules. 1976 Nov-Dec;9(6):945–950. doi: 10.1021/ma60054a013. [DOI] [PubMed] [Google Scholar]
- Thomas P. D., Dill K. A. An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11628–11633. doi: 10.1073/pnas.93.21.11628. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Torda A. E. Perspectives in protein-fold recognition. Curr Opin Struct Biol. 1997 Apr;7(2):200–205. doi: 10.1016/s0959-440x(97)80026-7. [DOI] [PubMed] [Google Scholar]
- Ulrich P., Scott W., van Gunsteren W. F., Torda A. E. Protein structure prediction force fields: parametrization with quasi-newtonian dynamics. Proteins. 1997 Mar;27(3):367–384. doi: 10.1002/(sici)1097-0134(199703)27:3<367::aid-prot5>3.0.co;2-a. [DOI] [PubMed] [Google Scholar]