Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection

Nucleic Acids Research

Volumn 34, Issue 17, 2006, Pages

  Chivian, Dylan ^a,c   Baker, David ^a,b  

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

^b UNIVERSITY OF WASHINGTON   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; ENERGY; INTERNET; PARAMETRIC TEST; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; EVALUATION; METHODOLOGY; STRUCTURAL HOMOLOGY;

AMINO ACID SEQUENCE; MODELS, MOLECULAR; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33750210515     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl480     Document Type: Article

References (87)

1. Vitkup,D., Melamud,E., Moult,J. and Sander,C. (2001) Completeness in structural genomics. Nature Struct. Biol., 8, 559-566.
2. Gribskov,M., McLachlan,A.D. and Eisenberg,D. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA, 84, 4355-4358.
3. Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
4. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
5. Rychlewski,L., Jaroszewski,L., Li,W. and Godzik,A. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
6. Jaroszewski,L., Rychlewski,L. and Godzik,A. (2000) Improving the quality of twilight-zone alignments. Protein Sci., 9, 1487-1496.
7. Heger,A. and Holm,L. (2001) Picasso: Generating a covering set of protein family profiles. Bioinformatics, 17, 272-279.
8. Yona,G. and Levitt,M. (2002) Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.
9. Sadreyev,R. and Grishin,N. (2003) COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
10. Edgar,R.C. and Sjolander,K. (2004) COACH: Profile-profile alignment of protein families using hidden Markov models. Bioinformatics, 20, 1309-1318.
11. Marti-Renom,M.A., Madhusudhan,M.S. and Sali,A. (2004) Alignment of protein sequences by their profiles. Protein Sci., 13, 1071-1087.
12. Fischer,D. and Eisenberg,D. (1996) Protein fold recognition using sequence-derived predictions. Protein Sci., 5, 947-955.
13. Jaroszewski,L., Rychlewski,L., Zhang,B. and Godzik,A. (1998) Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci., 7, 1431-1440.
14. Karplus,K.,Karchin,R., Barrett,C., Tu,S., Cline,M.,Diekhans,M.,Grate,L., Casper,J. and Hughey,R. (2001) What is the value added by human intervention in protein structure prediction? Proteins, Suppl 5, 86-91.
15. Shi,J., Blundell,T.L. and Mizuguchi,K. (2001) FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243-257.
16. Kelley,L.A., MacCallum,R.M. and Sternberg,M.J. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol., 299, 499-520.
17. Jones,D.T. (1999) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol., 287, 797-815.
18. Panchenko,A.R., Marchler-Bauer,A. and Bryant,S.H. (2000) Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol., 296, 1319-1331.
19. Contreras-Moreira,B., Fitzjohn,P.W. and Bates,P.A. (2003) In silico protein recombination: Enhancing template and sequence alignment selection for comparative protein modelling. J. Mol. Biol., 328, 593-608.
20. John,B. and Sali,A. (2003) Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res., 31, 3982-3992.
21. Saqi,M.A. and Sternberg,M.J. (1991) A simple method to generate non-trivial alternate alignments of protein sequences. J. Mol. Biol., 219, 727-732.
22. Zuker,M. (1991) Suboptimal sequence alignment in molecular biology. Alignment with error analysis. J. Mol. Biol., 221, 403-420.
23. Naor,D. and Brutlag,D.L. (1994) On near best possible alignments of biological sequences. J. Comput. Biol., 1, 349-366.
24. Jaroszewski,L., Li,W. and Godzik,A. (2002) In search for more accurate alignments in the twilight zone. Protein Sci., 11, 1702-1713.
25. Muckstein,U., Hofacker,I.L. and Stadler,P.F. (2002) Stochastic pairwise alignments. Bioinformatics, 18, S153-S160.
26. Petrey,D., Xiang,Z., Tang,C.L., Xie,L., Gimpelev,M., Mitros,T., Soto,C.S., Goldsmith-Fischman,S., Kernytsky,A., Schlessinger,A. et al. (2003) Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins, 53, 430-435.
27. Waterman,M.S., Eggert,M. and Lander,E. (1992) Parametric sequence comparisons. Proc. Natl Acad. Sci. USA, 89, 6090-6093.
28. Waterman,M.S. (1994) Parametric and ensemble sequence alignment algorithms. Bull. Math. Biol., 56, 743-767.
29. Pawlowski,K., Jaroszewski,L., Bierzynski,A. and Godzik,A. (1997) Multiple model approach - dealing with alignment ambiguities in protein modeling. Pac. Symp. Biocomput., 328-339.
30. Saqi,M.A., Bates,P.A. and Sternberg,M.J. (1992) Towards an automatic method of predicting protein structure by homology: An evaluation of suboptimal sequence alignments. Protein Eng., 5, 305-311.
31. Fischer,D. (2003) 3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor. Proteins, 51, 434-441.
32. Ginalski,K., Elofsson,A., Fischer,D. and Rychlewski,L. (2003) 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
33. Kosinski,J., Gajda,M.J., Cymerman,I.A., Kurowski,M.A., Pawlowski,M., Boniecki,M., Obarska,A., Papaj,G., Sroczynska-Obuchowicz,P., Tkaczuk,K.L. et al. (2005) FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6. Proteins, 61, 106-113.
34. Prasad,J.C., Vajda,S. and Camacho,C.J. (2004) Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Res., 32, W50-W54.
35. Venclovas,C. and Margelevicius,M. (2005) Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment and structure assessment. Proteins, 61, 99-105.
36. Wallner,B. and Elofsson,A. (2005) Pcons5: Combining consensus, structural evaluation and fold recognition scores. Bioinformatics, 21, 4248-4254.
37. Summers,N.L. and Karplus,M. (1990) Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/ deletion regions and Pro - non-Pro mutations. J. Mol. Biol., 216, 991-1016.
38. Fiser,A., Do,R.K. and Sali,A. (2000) Modeling of loops in protein structures. Protein Sci., 9, 1753-1773.
39. de Bakker,P.I., DePristo,M.A., Burke,D.F. and Blundell,T.L. (2003) 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, 51, 21-40.
40. Rohl,C.A., Strauss,C.E., Chivian,D. and Baker,D. (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins, 55, 656-677.
41. Jacobson,M.P., Pincus,D.L., Rapp,C.S., Day,T.J., Honig,B., Shaw,D.E. and Friesner,R.A. (2004) A hierarchical approach to all-atom protein loop prediction. Proteins, 55, 351-367.
42. Lee,M.R., Tsai,J., Baker,D. and Kollman,P.A. (2001) Molecular dynamics in the endgame of protein structure prediction. J. Mol. Biol., 313, 417-430.
43. Fan,H. and Mark,A.E. (2004) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci., 13, 211-220.
44. Misura,K.M. and Baker,D. (2005) Progress and challenges in high-resolution refinement of protein structure models. Proteins, 59, 15-29.
45. Taylor,W.R. (1999) Protein structural domain identification. Protein Eng., 12, 203-216.
46. Pearl,F., Todd,A., Sillitoe,I., Dibley,M., Redfern,O., Lewis,T., Bennett,C., Marsden,R., Grant,A., Lee,D. et al. (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res., 33, D247-D251.
47. Schaffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
48. Jaroszewski,L., Rychlewski,L., Li,Z., Li,W. and Godzik,A. (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res., 33, W284-W288.
49. Bellman,R. (1952) On the theory of dynamic programming. Proc. Natl Acad. Sci. USA, 38, 716-719.
50. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
51. Hirschberg,D.S. (1975) Linear space algorithm for computing maximal common subsequences. Commun. ACM, 18, 341-343.
52. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
53. Altschul,S.F. and Erickson,B.W. (1986) Optimal sequence alignment using affine gap costs. Bull. Math. Biol., 48, 603-616.
54. Myers,E.W. and Miller,W. (1988) Optimal alignments in linear space. Comput. Appl. Biosci., 4, 11-17.
55. Chivian,D., Kim,D.E., Malmstrom,L., Bradley,P., Robertson,T., Murphy,P., Strauss,C.E., Bonneau,R., Rohl,C.A. and Baker,D. (2003) Automated prediction of CASP-5 structures using the Robetta server. Proteins, 53, 524-533.
56. Holm,L. and Sander,C. (1996) Mapping the protein universe. Science, 273, 595-603.
57. Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
58. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
59. Bradley,P., Chivian,D., Meiler,J., Misura,K.M., Rohl,C.A., Schief,W.R., Wedemeyer,W.J., Schueler-Furman,O., Murphy,P., Schonbrun,J. et al. (2003) Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation. Proteins, 53, 457-468.
60. Chivian,D., Kim,D.E., Malmstrom,L., Schonbrun,J., Rohl,C.A. and Baker,D. (2005) Prediction of CASP6 structures using automated Robetta protocols. Proteins, 61, 157-166.
61. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
62. Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
63. Park,J., Karplus,K., Barrett,C., Hughey,R., Haussler,D., Hubbard,T. and Chothia,C. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
64. Canutescu,A.A. and Dunbrack,R.L.,Jr (2003) Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci., 12, 963-972.
65. Rohl,C.A., Strauss,C.E., Misura,K.M. and Baker,D. (2004) Protein structure prediction using Rosetta. Methods Enzymol., 383, 66-93.
66. Kuhlman,B. and Baker,D. (2000) Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA, 97, 10383-10388.
67. Sauder,J.M., Arthur,J.W. and Dunbrack,R.L.,Jr (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins, 40, 6-22.
68. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
69. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
70. Rychlewski,L. and Fischer,D. (2005) LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction. Protein Sci., 14, 240-245.
71. Ortiz,A.R., Strauss,C.E. and Olmea,O. (2002) MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison. Protein Sci., 11, 2606-2621.
72. Siew,N., Elofsson,A., Rychlewski,L. and Fischer,D. (2000) MaxSub: An automated measure for the assessment of protein structure prediction quality. Bioinformatics, 16, 776-785.
73. Plewczynski,D., Pas,J., von Grotthuss,M. and Rychlewski,L. (2002) 3D-Hit: Fast structural comparison of proteins. Appl. Bioinformatics, 1, 223-225.
74. Simons,K.T., Kooperberg,C., Huang,E. and Baker,D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
75. Dunbrack,R.L.,Jr and Cohen,F.E. (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci., 6, 1661-1681.
76. Shortle,D., Simons,K.T. and Baker,D. (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl Acad. Sci. USA, 95, 11158-11162.
77. Bonneau,R., Strauss,C.E. and Baker,D. (2001) Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins, 43, 1-11.
78. Wallner,B., Fang,H. and Elofsson,A. (2003) Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins, 53, 534-541.
79. Prasad,J.C., Comeau,S.R., Vajda,S. and Camacho,C.J. (2003) Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics, 19, 1682-1691.
80. Kim,D.E., Chivian,D. and Baker,D. (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res., 32, W526-W531.
81. Tramontano,A., Leplae,R. and Morea,V. (2001) Analysis and assessment of comparative modeling predictions in CASP4. Proteins, Suppl 5, 22-38.
82. Sippl,M.J., Lackner,P., Domingues,F.S., Prlic,A., Malik,R., Andreeva,A. and Wiederstein,M. (2001) Assessment of the CASP4 fold recognition category. Proteins, Suppl 5, 55-67.
83. Kinch,L.N., Wrabl,J.O., Krishna,S.S., Majumdar,I., Sadreyev,R.I., Qi,Y., Pei,J., Cheng,H. and Grishin,N.V. (2003) CASP5 assessment of fold recognition target predictions. Proteins, 53, 395-409.
84. Fischer,D., Rychlewski,L., Dunbrack,R.L.,Jr, Ortiz,A.R. and Elofsson,A. (2003) CAFASP3: The third critical assessment of fully automated structure prediction methods. Proteins, 53, 503-516.
85. Rychlewski,L., Fischer,D. and Elofsson,A. (2003) LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins, 53, 542-547.
86. Wang,G., Jin,Y. and Dunbrack,R.L.,Jr (2005) Assessment of fold recognition predictions in CASP6. Proteins, 61, 46-66.
87. Zemla,A. (2003) LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.