Stochastic pairwise alignments and scoring methods for comparative protein structure modeling

Journal of Chemical Information and Modeling

Volumn 47, Issue 3, 2007, Pages 1263-1270

  Marko, Adam C ^a   Stafford, Kate ^a   Wymore, Troy ^a  

^a PITTSBURGH SUPERCOMPUTING CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; POTENTIAL ENERGY; PROBLEM SOLVING; PROTEINS; STATISTICAL METHODS;

DISTANT HOMOLOGY; PAIRWISE ALIGNMENTS; SCORING METHODS; TEMPLATE STRUCTURES;

RANDOM PROCESSES;

PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; PROTEIN CONFORMATION; STATISTICS;

MODELS, CHEMICAL; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; STOCHASTIC PROCESSES;

EID: 34250854078     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600485s     Document Type: Article

References (47)

1. Chayen, N. E. Turning Protein Crystallization from an Art into a Science. Curr. Opin. Struct. Biol. 2004, 14, 577-583.
2. Chandonia, J.-M.; Brenner, S. E. The Impact of Structural Genomics: Expectations and Outcomes. Science 2006, 311, 347-351.
3. Baker, D.; Sali, A. Protein Structural Prediction and Structural Genomics. Science 2001, 294, 93-96.
4. Ginalski, K.; Grishin, N. V.; Godzik, A.; Rychlewski, L. Practical Lessons from Protein Structure Prediction. Nucleic Acids Res. 2005, 33, 1874-1891.
5. Dunbrack, R. L., Ir. Sequence Comparison and Protein Structure Prediction. Curr. Opin. Struct. Biol. 2006, 16, 374-384.
6. Jaroszewski, L.; Pawlowski, K.; Godzik, A. A Multiple Model Approach: Exploring the Limits of Comparative Modeling. J. Mol. Model. 1998, 4, 294-309.
7. Needlemen, S. B.; Wunsch, C. D. A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins. J. Mot. Biol. 1970, 48, 443-53.
8. Smith, T. F.; Waterman, M. S. Identification of Common Molecular Subsequences. J. Mol. Biol. 1981, 147, 195-197.
9. Henikoff, S.; Henikoff, J. G. Amino Acid Substitution Matrices. Adv. Protein Chem. 2000, 54, 73-97.
10. Vogt, G.; Etzold, T.; Argos, P. An Assessment of Amino Acid Exchange Matrices in Aligning Protein Sequences: The Twilight Zone Revisited. J. Mol. Biol. 1995, 249, 816-31.
11. Jaroszewski, L.; Weizhong, L.; Godzik, A. In Search for More Accurate Alignments in the Twilight Zone. Protein Sci. 2002, 11, 1702-1713.
12. Vingron, M. Near Optimal Sequence Alignment. Curr. Opin. Struct. Biol. 1996, 6, 346-352.
13. Saqi, M. A.; Sternberg, M. J. A Simple Method to Generate Nontrivial Alignments of Protein Sequences. J. Mol. Biol. 1991, 219, 727-732.
14. Naor, D.; Brutlag, D. L. On Near-optimal Alignments of Biological Sequences. J. Comput. Biol. 1994, 1, 349-66.
15. Mückstein, U.; Holfacker, I. L.; Stadler, P. F. Stochastic Pairwise Alignments. Bioinformatics 2002, 18, S153-S160.
16. Miyazawa, S. A Reliable Sequence Alignment Method Based on Probabilities of Residues Correspondences. Protein Eng. 1994, 8, 999-1009.
17. Kschischo, M.; Lassig, M. Finite-temperature Sequence Alignment. Pac. Symp. Biocomputing 2000, 1, 624-635.
18. Contreras-Moreira, B.; Fitzjohn, P. W.; Bates, P. In Silico Protein Recombination: Enhancing Template and Sequence Alignment Selection for Comparative Protein Modeling. J. Mol. Biol. 2003, 328, 593-608.
19. Rai, B. K.; Fiser, A. Multiple Mapping Method: A Novel Approach to the Sequence-to-Structure Alignment Problem in Comparative Protein Structure Modeling. Proteins: Struct., Funct., Bioinf. 2006, 63, 644-661.
20. John, B.; Sali, A. Comparative Protein Structure Modeling by Iterative Alignment, Model Building and Model Assessment. Nucleic Acids Res. 2003, 31, 3982-3992.
21. Chivian, D.; Baker, D. Homology Modeling using Parametric Alignment Ensemble Generation with Consensus and Energy-based Model Selection. Nucleic. Acids Res. 2006, 00(00), e2-18.
22. Melo, F.; Sanchez, R.; Sali, A. Statistical Potentials for Fold Assessment. Protein Sci. 2002, 11, 430-448.
23. Sippl, M. J. Recognition of Three-dimensional Structures of Proteins. Proteins 1993, 17, 355-362.
24. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. 1998, 102, 3586-3616.
25. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
26. Lee, M. S; Feig, M; Salsbury, F. R., Jr.; Brooks, C. L., III. New Analytic Approximation to the Standard Molecular Volume Definition and its Application to Generalized Born Calculations. J. Comput. Chem. 2003, 24, 1348-1356.
27. Tsui, V.; Case, D. Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model. J. Am. Chem. Soc. 2000, 1222, 2489-2498.
28. Fiser, A.; Feig, M.; Brooks, C. L., III; Sali, A. Evolution and Physics in Comparative Protein Structure Modeling. Acc. Chem. Res. 2002, 35, 413-421.
29. Bradley, P.; Misura, K. M. S.; Baker, D. Toward High-resolution De Novo Structure Prediction for Small Proteins. Science 2005, 309, 1868-1871.
30. Zemla, A. LGA: A Method for Finding 3D Similarities in Protein Structures. Nucleic Acids Res. 2003, 31, 3370-3374.
31. Kinch, L. N.; Qi, Y.; Hubbard, T. J. P.; Grishin, N. V. CASP5 Target Classification. Proteins 2003, 53, Suppl. 6, 340-351.
32. Tress, M.; Ezkurdia, I.; Grana, O.; Lopez, G.; Valencia, A. Assessment of Predictions Submitted for the CASP6 Comparative Modeling Category. Proteins 2005, 61, Suppl. 7, 27-45.
33. Hunt, L. T.; Barker, W. C.; Schwartz, R. M.; Orcutt, B. C.; Young, C. L. In Atlas of Protein Sequence and Structure; Dayhoff, M. O., Ed.; National Biomedical Research Foundation: Washington, DC, 1978; Vol. 5, Suppl. 3, pp 345-352.
34. Gonnet, G. H.; Cohen, M. A.; Benner, S. A. Exhaustive Matching of the Entire Protein Sequence Database. Science 1992, 256, 1443-1445.
35. Benner, S. A.; Cohen, M. A.; Gonnet, G. H. Amino Acid Substitution During Functionally Constrained Divergent Evolution of Protein Sequences. Protein. Eng. 1994, 7, 1323-32.
36. Sali, A.; Blundell, T. L. Comparative Protein Modelling by Satisfaction of Spatial Restraints. J. Mol. Biol. 1993, 234, 779-815.
37. Humphrey, W.; Dalke, A.; Schulten, K. VMD - Visual Molecular Dynamics. J. Mol. Graphics Modell. 1996, 14, 33-38.
38. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera - A Visualization System for Exploratory Research and Analysis. J. Comput. Chem. 2004, 25, 1605-1612.
39. 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.
40. Zhang, C.; Liu, S.; Zhou, H.; Zhou, Y. The Dependence of All-atom Statistical Potentials on Structural Training Database. Biophys. J. 2004, 86, 3349-3358.
41. Shen, M. Y.; Sali, A. Statistical Potential for the Assessment and Prediction of Protein Structures. Protein Sci. 2006, 15, 2507-2524.
42. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187-217.
43. Feig, M; Karanicolas, J.; Brooks, C. L.; 3rd. MMTSB Tool Set: Enhanced Sampling and Multiscale Modeling Methods for Applications in Structural Biology. J. Mol. Graphics Modell. 2004, 22, 377-95.
44. Shindyalov, I. N.; Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 1998, 11, 739-47.
45. Marti-Renom, M. A.; Stuart, A.; Fiser, A;, Sanchez, R.; Melo, F.; Sali, A. Comparative Protein Structure Modeling of Genes and Genomes. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 291-325.
46. Offman, M. N.; Fitzjohn, P. W.; Bates, P. A. Developing a move-set for protein model refinement. Bioinformatics 2006, 22, 1838-1845.
47. Chothia, C.; Lesk, A. M. The Relation Between the Divergence of sequence and structure in proteins. EMBO J. 1986, 5, 823-826.