A model of local-minima distribution on conformational space and its application to protein structure prediction

Proteins: Structure, Function and Genetics

Volumn 64, Issue 4, 2006, Pages 985-991

  Li, Hongzhi ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; ENERGY ABSORPTION; MATHEMATICAL COMPUTING; MATHEMATICAL PARAMETERS; METHODOLOGY; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; PROTEIN FOLDING; THEORETICAL MODEL;

PROTEIN;

MODELS, THEORETICAL; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 33748448474     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21084     Document Type: Article

References (15)

1. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculation. J Comput Chem 1983;4:187-217.
2. Bryngelson J, Wolynes PG. Spin-glass and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 1987;84:7524-7528.
3. DePristo MA, de Bakker PIW, Lovell SC, Blundell TL. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins 2003;51:41-55.
4. Dill KA. Polymer principles and protein folding. Protein Sci 1999;8:1166-1180.
5. Jacobson MP, Pincus DL, Rapp CS, Day TJF, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins 2004;55:351-367.
6. Jorgensen WL, Tirado-Rives J. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
7. Li H, Zhou Y. Fold helical proteins by energy minimization in dihedral space and a DFIRE-based statistical energy function. J Bioinfo Comput Biol 2005;3:1151-1170.
8. Li H, Zhou Y. SCUD: fast structure clustering of decoys using reference state to remove overall rotation. J Comput Chem 2005;26:1189-1192.
9. Northby JA. Structure and binding of Lennard-Jones clusters: 13 < N < 147. J Chem Phys 1987;87:6166-6177.
10. Onuchic JN, Luthy-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 1997;48:545-600.
11. Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 1998;95:11158-11162.
12. Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio structure prediction. Biophys J 2003;85:1145-1164.
13. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004;25:865-871.
14. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726
15. Correction. Protein Sci. 2003;12:2121