Calculation of protein conformation by global optimization of a potential energy function

Proteins: Structure, Function and Genetics

Volumn 37, Issue SUPPL. 3, 1999, Pages 204-208

  Lee, Jooyoung ^a   Liwo, Adam ^a,b   Ripoll, Daniel R ^a   Pillardy, Jaroslaw ^a   Scheraga, Harold A ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF GDA SK   (Poland)

Author keywords

Conformational search; Global optimization; Potential energy function; Protein folding; Structure prediction

Indexed keywords

GLOBULAR PROTEIN; PROTEIN; PEPTIDE FRAGMENT;

AMINO ACID SEQUENCE; ARTICLE; ATOM; CALCULATION; CONTROLLED STUDY; ENERGY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN TARGETING; THERMODYNAMICS; ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN SECONDARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS;

EID: 0032605909     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0134(1999)37:3+<204::aid-prot26>3.0.co;2-f     Document Type: Article

References (21)

1. Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
2. Scheraga HA. Recent developments in the theory of protein folding: searching for the global energy minimum. Biophys Chem 1996;59:329-339.
3. Mirny LA, Shakhnovich EI. Protein structure prediction by threading. Why it works and why it does not. J Mol Biol 1998;283:507-526.
4. Lee J, Liwo A, Scheraga HA. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc Natl Acad Sci USA 1999;96:2025-2030.
5. Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide. Protein Sci 1993;2:1715-1731.
6. Liwo A, Oldziej S, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. A united-residue force field for off-lattice protein-structure simulations: I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J Comput Chem 1997;18:849-873.
7. Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Oldziej S, Scheraga HA. A united-residue force field for off-lattice protein-structure simulations: II. Parameterization of short-range interactions and determination of the weights of energy terms by Z-score optimization. J Comput Chem 1997;18:874-887.
8. Liwo A, Kazmierkiewicz R, Czaplewski C, Groth M, Oldziej S, Wawak RJ, Rackovsky S, Pincus MR, Scheraga HA. United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J Comput Chem 1998;19:259-276.
9. Lee J, Scheraga HA, Rackovsky S. New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J Comput Chem 1997;18:1222-1232.
10. Lee J, Scheraga HA, Rackovsky S. Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers 1998;46:103-115.
11. Lee J, Scheraga HA. Conformational space annealing by parallel computations: extensive conformational search of Met-enkephalin and of the 20-residue membrane-bound portion of melittin. Int J Quant Chem; in press.
12. Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment. Protein Sci 1993; 2:1697-1714.
13. Ripoll DR, Liwo A, Scheraga HA. New developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin. Biopolymers 1998;46:117-126.
14. Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 1992;96:6472-6484.
15. Vila J, Williams RL, Vásquez M, Scheraga HA. Empirical solvation models can be used to differentiate native from near-native conformations for bovine pancreatic trypsin inhibitor. Proteins 1991;10:199-218.
16. Späth H. Cluster analysis algorithms. New York: Halsted Press; 1980. p 170-194.
17. Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I. CASP3: Analysis of ab initio 3D prediction and secondary structure prediction. Proteins Suppl 1999;3:149-170.
18. Yang F, Gustafson KR, Boyd MR, Wlodawer A. Crystal structure of Escherichia coli HdeA. Nature Struct Biol 1998;5:763-764.
19. Third Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. Pacific Grove, CA: Asilomar Center. December 13-17, 1998. (http://predictioncenter.llnl.gov/casp3/Casp3.html).
20. Golub GH, Van Loan CF. Matrix computations. Baltimore, MD: The Johns Hopkins University Press; 1987. p 293-294.
21. http://predictioncenter.llnl.gov/casp3/results/SS-browser/ss_res. cgi.