Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments

Proteins: Structure, Function and Genetics

Volumn 58, Issue 2, 2005, Pages 321-328

  Zhou, Hongyi ^a   Zhou, Yaoqi ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

Fold recognition; Protein structure prediction; Protein threading; Sequence profile

Indexed keywords

DNA FRAGMENT;

ACCURACY; ARTICLE; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; QUALITY CONTROL; SEQUENCE HOMOLOGY; TIME;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EVOLUTION; EVOLUTION, MOLECULAR; MODELS, STATISTICAL; PEPTIDE LIBRARY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; TIME FACTORS;

EID: 11344292852     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20308     Document Type: Article

References (77)

1. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
2. Dayhoff MO, Barker WC, Hunt LT. Establishing homologies in protein sequences. Meth Enzymol 1983;91:524-545.
3. Pearson WR, Lipman DJ. Improved tools for biological sequence analysis. Proc Natl Acad Sci USA 1988;85:2444-2448.
4. Altschul SF, Gish W, Miller W, Myers E, Lipman D. Basic local alignment tool. J Mol Biol 1990;215:403-410.
5. Vingron M, Waterman MS. Sequence alignment and penalty choice. Review of concepts, case studies and implications. J Mol Biol 1994;235:1-12.
6. Qian B, Goldstein RA. Optimization of a new score function for the generation of accurate alignments. Proteins 2002;48:605-610.
7. Teodorescu O, Galor T, Pillardy J, Elber R. Enriching the sequence substitution matrix by structural information. Proteins 2004;54:41-48.
8. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
9. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
10. Henikoff S, Henikoff JG. Amino acid substitutes matrices from protein blocks. Proc Natl Acad Sci 1992;89:10915-10919.
11. Bailey TL, Gribskov M. Score distributions for simultaneous matching to multiple motifs. J Comput Biol 1997;4:45-59.
12. Koretke KK, Russell RB, Lupas AN. Fold recognition from sequence comparisons. Proteins 2001;Suppl 5:68-75.
13. Eddy SR. Profile hidden Markov models. Bioinformatics 1998;14:755-763.
14. Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci USA 1987;84:4355-4358.
15. Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000;9:232-241.
16. Yona G, Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol 2002;315:1257-1275.
17. Marti-Renom MA, Madhusudhan M, Sali A. Alignment of protein sequences by their profiles. Protein Sci 2004;13:1071-1087.
18. Mittelman D, Sadreyev R, Grishin N. Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics 2003;19:1531-1539.
19. Wang G, Dunbrack RL Jr. Scoring profile-profile sequence alignments. Protein Sci 2004;13:1612-1626.
20. Bowie JW, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
21. Godzik A, Skolnick J. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc Natl Acad Sci USA 1992;89:12098-12102.
22. Bryant SH, Lawrence CE. An empirical energy function for threading protein sequence through the folding motif. Proteins 1993;16:92-112.
23. Abagyan R, Frishman D, Argos P. Recognition of distantly related proteins through energy calculations. Proteins 1994;19:132-140.
24. Murzin AG, Bateman A. Distance homology recognition using structural classification of proteins. Proteins 1997;Suppl. 1:105-112.
25. Xu Y, Xu D. Protein threading using PROSPECT: Design and evaluation. Proteins 2000;40:343-354.
26. Jones DT. Progress in protein structure prediction. Curr Opin Struct Biol 1997;7:377-387.
27. Torda AE. Perspectives in protein-fold recognition. Curr Opin Struct Biol 1997;7:200-205.
28. David R, Korenberg MJ, Hunter IW. 3D-1D threading methods for protein fold recognition. Pharmacogenomics 2000;1:445-455.
29. Sippl MJ, Lackner P, Domingues FS, Prlić A, Malik R, Andreeva A, Wiederstein M. Assessment of the CASP4 fold recognition category. Proteins 2001; Suppl 5:55-67.
30. Meller J, Elber R. Protein recognition by sequence-to-structure fitness: bridging efficiency and capacity of threading models. Adv Chem Phys 2002;120:77-130.
31. Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins 2001;42:319-331.
32. Yi TM, Lander ES. Recognition of related proteins by iterative template refinement (ITR). Protein Sci 1994;3:1315-1328.
33. Elofsson A, Fischer D, Rice DW, Le Grand SM, Eisenberg D. A study of combined structure/sequence profiles. Fold Des 1996;1:451-461.
34. Fischer D, Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci 1996;5:947-955.
35. Rost B, Sander C. Protein fold recognition by prediction-based threading. J Mol Biol 1997; 270:471-480.
36. Jaroszewski L, Rychlewski L, Zhang B, Godzik A. Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci 1998;7:1431-1440.
37. Kelley LA, MacCallum RM, Sternberg MJE. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000;299:499-520.
38. Panchenko AR, Marchler-Bauer A, Bryant SH. Combination of threading potentials and sequence profiles improves fold recognition. J Mol Biol 2000;296:1319-1331.
39. Shan YB, Wang GL, Zhou HX. Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading. Proteins 2001;42:23-37.
40. Al-Lazikani B, Sheinerman FB, Honig B. Combining multiple structure and sequence alignments to improve sequence detection and alignment: Application to the SH2 domains of Janus kinases. Proc Natl Acad Sci USA 2001;98:14796-14801.
41. Kim D, Xu D, Guo J, Ellrott K, Xu Y. PROSPECT II: Protein structure prediction program for the genome-scale. Protein Eng 2003;16:641-650.
42. Tang CL, Xie L, Koh IY, Posy S, Alexov E, Honig B. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol 2003;334:1043-1062.
43. Zhou H, Zhou Y. Single-body knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004;55:1005-1013.
44. Ogata K, Ohya M, Umeyama H. Amino acid similarity matrix for homology derived from structural alignment and optimized by the Monte Carlo method. J Mol Graph Model 1998;16:178-189.
45. Prlic A, Domingues FS, Sippl MJ. Structure-derived substitution matrices for alignment of distantly related sequences. Protein Eng 2000;13:545-550.
46. Blake JD, Cohen FE. Pairwise sequence alignment below the twilight zone. J Mol Biol 2001;307:721-735.
47. Shi J, Blundell TL, Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001;310:243-257.
48. Gough J, Karplus K, Hughey R, Chothia C. Assignment of homology to genome sequences using a library of hidden markov models that represent all proteins of known structure. J Mol Biol 2001;313.
49. Panchenko AR, Bryant SH. A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci 2002;11:361-370.
50. Gough J, Chothia C. Superfamily:HMMs representing all proteins of known structure. Scop sequence searches, alignments, and genome assignments. Nucleic Acids Res 2002;30:268-272.
51. Griffiths-Jones S, Bateman A. The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs. Bioinformatics 2002;18:1243-1249.
52. Lindahl E, Elofsson A. Identification of related proteins on family, superfamily and fold level. J Mol Biol 2000;295:613-625.
53. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. Livebench-1: large-scale automated evaluation of protein structure prediction servers. Protein Sci 2001;10:352-361.
54. Ginalski K, Pas J, Wyrwicz LS, vonGrotthuss M, Bujnicki JM, Rychlewski L. ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res 2003;31:3804-3807.
55. Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP) - Round V. Proteins 2003;53:334-339.
56. Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 2003;51:434-441.
57. Fischer D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. In: Altman RB, Dunker AK, Hunter L, Klein TE, editors. Pacific Symp. Biocomputing. New York: World Scientific; 2000. p 119-130.
58. Godzik A. The structural alignment between two proteins: is there a unique answer? Protein Sci 1996;5:1325-1338.
59. Chakravarty S, Varadarajan R. Residue depth: a novel parameter for the analysis of protein structure and stability. Strucure Fold Des 1999;15:723-732.
60. 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.
61. Wang G, Dunbrack RL Jr. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
62. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
63. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
64. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
65. Siew N, Elofsson A, Rychlewski L, Fischer D. Maxsub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000;16:776-785.
66. Domingues FS, Lackner P, Andreeva A, Sippl MJ. Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J Mol Biol 2000;297:1003-1013.
67. Shindyalov IN, Bourne P. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998;11:739-747.
68. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure 2002;10:435-440.
69. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
70. Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004;55:502-518.
71. Wallner B, Fang H, Elofsson A. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins 2003;53:534-541.
72. Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss C. E, Bonneau R, Rohl CA, Baker D. Automated prediction of casp-5 structures using the robetta server. Proteins 2003;53:524-533.
73. Du P, Andrec M, Levy RM. Have we seen all structures corresponding to short protein fragments in the protein data bank? An update. Protein Eng 2003;16:407-414.
74. Ye Y, Jaroszewski L, LiW, Godzik A. A segment alignment approach to protein comparison. Bioinformatics 2003;19:742.
75. Hughey R, Krogh A. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci 1996;12:95-107.
76. Edgar RC, Sjolander K. Simultaneous sequence alignment and tree construction using hidden markov models. Pac Symp Biocomput 2003;180-191.
77. Xu J, Li M, Kim D, Xu Y. RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol 2003;1:95-117.