Long loop prediction using the protein local optimization program

Proteins: Structure, Function and Genetics

Volumn 65, Issue 2, 2006, Pages 438-452

  Zhu, Kai ^a   Pincus, David L ^a   Zhao, Suwen ^a   Friesner, Richard A ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

Conformational sampling; Continuum solvation model; Hydrophobic; Loop prediction

Indexed keywords

ARTICLE; CONTINUUM SOLVATION MODEL; HYDROPHOBICITY; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; PROTON TRANSPORT; SOLVATION; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; HYDROPHOBICITY; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTONS; SOFTWARE DESIGN;

EID: 33748988479     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21040     Document Type: Article

References (31)

1. Jacobson MP, Pincus DL, Rapp CS, Day TJF, Honig B, Shaw DW, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins Struct Funct Bioinformat 2004;55:351-367.
2. Fiser A, Do RKG, Sali A. Modeling of loops in protein structures. Protein Sci 2000;9:1753-1773.
3. de Bakker PIW, Depristo MA, Burke DF, Blundell TL. Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins Struct Funct Bioinformat 2002;51:21-40.
4. Xiang ZX, Soto CS, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci USA 2002;99:7432-7437.
5. Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins Struct Funct Bioinformat 2004;55:656-677.
6. Monnigmann M, Floudas CA. Protein loop structure prediction with flexible stem geometries. Proteins Struct Funct Bioinformat 2005;61:748-762.
7. Hartigan JA. Clustering algorithms. New York: Wiley; 1975.
8. Hartigan JA, Wong MA. Algorithm AS 136: a K-means clustering algorithm. Appl Stat 1979;28:100-108.
9. Jorgensen WL, Maxwell DS, TiradoRives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;118: 11225-11236.
10. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 2001;105:517-529.
11. Jacobson MP, Kaminski GA, Friesner RA, Rapp CS. Force field validation using protein side chain prediction. J Phys Chem B 2002;105:11673-11680.
12. Ghosh A, Rapp CS, Friesner RA. Generalized born model based on a surface integral formulation. J Phys Chem B 1998;102:10983-10990.
13. Gallicchio E, Zhang LY, Levy RM. The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel nonpolar hydration free energy estimator. J Comput Chem 2002;23:517-529.
14. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 1997;11:425-445.
15. Jacobson MP, Friesner RA, Xiang ZX, Honig B. On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol 2002;320:597-608.
16. Xiang ZX, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001;311:421-430.
17. Bruccoleri RE, Karplus M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 1987;26:137-168.
18. Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD. Improved Protein-ligand docking using GOLD. Proteins Struct Funct Bioinformat 2003;52:609-623.
19. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47:1739-1749.
20. Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 2004;47:1750-1759.
21. Wang GL, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
22. DePristo MA, de Bakker PIW, Lovell SC, Blundell TL. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins Struct Funct Bioinformat 2003;51:41-55.
23. Xin L. Advances in high resolution protein structure modeling. New York: Columbia University; 2005.
24. Lee MS, Salsbury FR Jr, Brooks CL. Novel generalized Born Methods. J Chem Phys 2002;116:10606-10614.
25. Romanov AN, Jabin SN, Martynov YB, Sulimov AV, Grigoriev FV, Sulimov VB. Surface Generalized Born Method: a simple, fast and precise implicit solvent model beyond the Coulomb approxiMation. J Phys Chem A 2004;108:9323-9327.
26. Wojciechowski M, Lesyng B. Generalized Born Model: analysis, refinement, and applications to proteins. J Phys Chem B 2004;108: 18368-18376.
27. Yu Z, Jacobson MP, Rapp CS, Friesner RA. First shell solvation of ion pairs: correction of systematic errors in implicit solvent models. J Phys Chem B 2004;108:6643-6654.
28. Levy RM, Zhang LY, Gallicchio E, AK F. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. J Am Chem Soc 2003;125:9523-9530.
29. Felts AK, Harano Y, Gallicchio E, RM L. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins Struct Funct Bioinformat 2004;56:310-321.
30. Gallicchio E, RM L. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J Comp Chem 2004;25:479-499.
31. Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM. Integrated modeling program, applied chemical theory (IMPACT). J Comp Chem 2005;26:1752-1780.