Improved protein structure selection using decoy-dependent discriminatory functions

BMC Structural Biology

Volumn 4, Issue , 2004, Pages 1-18

  Wang, Kai ^a   Fain, Boris ^b   Levitt, Michael ^b   Samudrala, Ram ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; DENSITY; MATHEMATICAL COMPUTING; PREDICTION; PROTEIN FUNCTION; PROTEIN STRUCTURE; BIOLOGY; CHEMISTRY; METHODOLOGY; PREDICTIVE VALUE; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN QUATERNARY STRUCTURE; STANDARD;

ESCHERICHIA COLI PROTEIN; RIBOSOME PROTEIN;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ESCHERICHIA COLI PROTEINS; PREDICTIVE VALUE OF TESTS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, QUATERNARY; RIBOSOMAL PROTEINS;

EID: 4544355522     PISSN: 14726807     EISSN: None     Source Type: Journal    
DOI: 10.1186/1472-6807-4-1     Document Type: Article

References (37)

1. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M: CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comput Chem 1983, 4:187-217. Return to citation in text: [1]
2. Jorgensen William L., Tirado-Rives Julian: The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 1988, 110:1657-1666. Return to citation in text: [1]
3. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA: A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995, 117:5179-5197. Return to citation in text: [1]
4. Fain B, Xia Y, Levitt M: Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Protein Sci 2002, 11:2010-2021. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
5. Holm L, Sander C: Evaluation of protein models by atomic solvation preference. J Mol Biol 1992, 225:93-105. [PubMed Abstract] Return to citation in text: [1] [2]
6. Subramaniam S, Tcheng DK, Fenton JM: A knowledge-based method for protein structure refinement and prediction. Proc Int Conf Intell Syst Mol Biol 1996, 4:218-229. [PubMed Abstract] Return to citation in text: [1] [2]
7. Samudrala R, Moult J: An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998, 275:895-916. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2] [3] [4] [5]
8. Lu H, Skolnick J: A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001, 44:223-232. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2] [3] [4]
9. Berrera M, Molinari H, Fogolari F: Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 2003, 4:8. [PubMed Abstract] [BioMed Central Full Text] Return to citation in text: [1] [2] [3]
10. McConkey BJ, Sobolev V, Edelman M: Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci U S A 2003, 100:3215-3220. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2] [3] [4]
11. Wang Y, Zhang H, Li W, Scott RA: Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci U S A 1995, 92:709-713. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
12. Park B, Levitt M: Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996, 258:367-392. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2] [3]
13. Felts AK, Gallicchio E, Wallqvist A, Levy RM: Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model. Proteins 2002, 48:404-422. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
14. Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss CE, Baker D: Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins 2003, 53 Suppl 6:457-468. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
15. Skolnick J, Zhang Y, Arakaki AK, Kolinski A, Boniecki M, Szilagyi A, Kihara D: TOUCHSTONE: a unified approach to protein structure prediction. Proteins 2003, 53 Suppl 6:469-479. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
16. Jones DT, McGuffin LJ: Assembling novel protein folds from super-secondary structural fragments. Proteins 2003, 53 Suppl 6:480-485. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
17. Fang Q, Shortle D: Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments. Proteins 2003, 53 Suppl 6:486-490. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
18. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R: Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 2003, 53 Suppl 6:491-496. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
19. Moult J: Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol 1997, 7:194-199. [PubMed Abstract] [Publisher Full Text] Return to citation in text: [1] [2]
20. Kocher JP, Rooman MJ, Wodak SJ: Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 1994, 235:1598-1613. [PubMed Abstract] [Publisher Full Text] Return to citation in text: [1] [2]
21. Rooman MJ, Wodak SJ: Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng 1995, 8:849-858. [PubMed Abstract] Return to citation in text: [1] [2]
22. Thomas PD, Dill KA: Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol 1996, 257:457-469. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2]
23. Ben-Naim A: Statistical potentials extracted from protein structures: Are these meaningful potentials. J Chem Phys 1997, 107:3698-3706. [Publisher Full Text] Return to citation in text: [1] [2]
24. Huang ES, Samudrala R, Ponder JW: Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. J Mol Biol 1999, 290:267-281. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
25. Zhu Jiang, Zhu Qianqian, Shi Yunyu, Liu Haiyan: How well can we predict native contacts in proteins based on decoy structures and their energies? Proteins 2003, 52:598-608. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
26. Shortle D, Simons KT, Baker D: Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci U S A 1998, 95:11158-11162. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2]
27. Simons KT, Bonneau R, Ruczinski I, Baker D: Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 1999, Suppl 3:171-176. [PubMed Abstract] [Publisher Full Text] Return to citation in text: [1] [2] [3]
28. Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D: Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins 2001, Suppl 5:119-126. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2]
29. Samudrala R, Levitt M: Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000, 9:1399-1401. [PubMed Abstract] Return to citation in text: [1] [2] [3]
30. Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D: An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 2003, 53:76-87. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2] [3] [4]
31. Park BH, Huang ES, Levitt M: Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol 1997, 266:831-846. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2]
32. Gatchell DW, Dennis S, Vajda S: Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins 2000, 41:518-534. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
33. Huang ES, Samudrala R, Park BH: Scoring Functions for ab initio folding. Predicting Protein Structure: Methods and Protocols(Edited by: Walker J and Webster D). 2000. Return to citation in text: [1]
34. Samudrala R, Levitt M: A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol 2002, 2:3. [PubMed Abstract] [BioMed Central Full Text] Return to citation in text: [1] [2] [3]
35. Simons KT, Kooperberg C, Huang E, Baker D: Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997, 268:209-225. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1] [2]
36. Feig M, Brooks C. L., 3rd: Evaluating CASP4 predictions with physical energy functions. Proteins 2002, 49:232-245. [PubMed Abstract][Publisher Full Text] Return to citation in text: [1]
37. Samudrala R, Xia Y, Levitt M, Huang ES: A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pac Symp Biocomput 1999, 505-516. [PubMed Abstract] Return to citation in text: [1]