Estimating quality of template-based protein models by alignment stability

Proteins: Structure, Function and Genetics

Volumn 71, Issue 3, 2008, Pages 1255-1274

  Chen, Hao ^a   Kihara, Daisuke ^a,b  

^a PURDUE UNIVERSITY   (United States)

^b Purdue University   (United States)

Author keywords

Error estimation; Protein structure prediction; Quality assessment of protein models; Suboptimal alignment; Template based modeling; Threading

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STABILITY; PROTEIN STRUCTURE; QUALITY CONTROL; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT; THERMODYNAMICS;

EID: 42449093288     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21819     Document Type: Article

References (92)

1. Jones DT. Protein structure prediction in the postgenomic era. Curr Opin Struct Biol 2000;10:371-379.
2. Schonbrun J, Wedemeyer WJ, Baker D. Protein structure prediction in 2002. Curr Opin Struct Biol 2002;12:348-354.
3. Petrey D, Honig B. Protein structure prediction: inroads to biology. Mol Cell 2005;20:811-819.
4. Ginalski K. Comparative modeling for protein structure prediction. Curr Opin Struct Biol 2006;16:172-177.
5. Marti-Renom MA, Stuart AC, 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.
6. Xiang Z. Advances in homology protein structure modeling. Curr Protein Pept Sci 2006;7:217-227.
7. Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005;309:1868-1871.
8. Jacobson M, Sali A. Comparative protein structure modeling and its applications to drug discovery. Annu Rep Med Chem 2004;39:259-276.
9. Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Jr, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 2006;441:656-659.
10. Rosenberg M, Goldblum A. Computational protein design: a novel path to future protein drugs. Curr Pharm Des 2006;12:3973-3997.
11. Park S, Yang X, Saven JG. Advances in computational protein design. Curr Opin Struct Biol 2004;14:487-494.
12. Wilson CA, Kreychman J, Gerstein M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol 2000;297:233-249.
13. Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J 1986;5:823-826.
14. Hardin C, Pogorelov TV, Luthey-Schulten Z. Ab initio protein structure prediction. Curr Opin Struct Biol 2002;12:176-181.
15. Kihara D, Lu H, Kolinski A, Skolnick J. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci USA 2001;98:10125-10130.
16. Simons KT, Strauss C, Baker D. Prospects for ab initio protein structural genomics. J Mol Biol 2001;306:1191-1199.
17. Vincent JJ, Tai CH, Sathyanarayana BK, Lee B. Assessment of CASP6 predictions for new and nearly new fold targets. Proteins 2005;61 (Suppl):767-783.
18. Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins 2001;42:319-331.
19. 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.
20. Zhou H, Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004;55:1005-1013.
21. Wells GA, Birkholtz LM, Joubert F, Walter RD, Louw AI. Novel properties of malarial S-adenosylmethionine decarboxylase as revealed by structural modelling. J Mol Graph Model 2006;24:307-318.
22. Skowronek KJ, Kosinski J, Bujnicki JM. Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis. Proteins 2006;63:1059-1068.
23. Wojciechowski M, Skolnick J. Docking of small ligands to low-resolution and theoretically predicted receptor structures. J Comput Chem 2002;23:189-97.
24. Vakser IA. Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers 1996;39:455-464.
25. Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
26. Skolnick J, Fetrow JS, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol 2000;18:283-287.
27. Hawkins T, Kihara D. Function prediction of uncharacterized proteins. J Bioinform Comput Biol 2007;5:1-30.
28. Forster MJ. Molecular modelling in structural biology. Micron 2002;33:365-384.
29. Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003;374:461-491.
30. Bradley P, Malmstrom L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D. Free modeling with Rosetta in CASP6. Proteins 2005;61 (Suppl 7):128-134.
31. Jones DT. Predicting novel protein folds by using FRAGFOLD. Proteins 2001;Suppl 5:127-132.
32. Bonneau R, Strauss C, Rohl C, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. J Mol Biol 2002;322:65-78.
33. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure 1997;5:1093-108.
34. Tan YH, Huang H, Kihara D. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins 2006;64:587-600.
35. Kolinski A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins 2001;44:133-149.
36. Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001;44:223-232.
37. Wroblewska L, Skolnick J. Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. J Comput Chem 2007;28:2059-2066.
38. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
39. Eisenberg D, Luthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 1997;277:396-404.
40. Vingron M. Near-optimal sequence alignment. Curr Opin Struct Biol 1996;6:346-352.
41. Vingron M, Argos P. Determination of reliable regions in protein sequence alignments. Protein Eng 1990;3:565-569.
42. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970;48:443-453.
43. Chao KM, Hardison RC, Miller W. Locating well-conserved regions within a pairwise alignment. Comput Appl Biosci 1993;9:387-396.
44. Saqi MA, Sternberg MJ. A simple method to generate non-trivial alternate alignments of protein sequences. J Mol Biol 1991;219:727-732.
45. Sommer I, Toppo S, Sander O, Lengauer T, Tosatto SC. Improving the quality of protein structure models by selecting from alignment alternatives. BMC Bioinformatics 2006;7:364.
46. Miyazawa S. A reliable sequence alignment method based on probabilities of residue correspondences. Protein Eng 1995;8:999-1009.
47. Schlosshauer M, Ohlsson M. A novel approach to local reliability of sequence alignments. Bioinformatics 2002;18:847-854.
48. Zhang MQ, Marr TG. Alignment of molecular sequences seen as random path analysis. J Theor Biol 1995;174:119-129.
49. Kschischo M, Lassig M. Finite-temperature sequence alignment. Pac Symp Biocomput 2000;624-635.
50. Yu L, Smith TF. Positional statistical significance in sequence alignment. J Comput Biol 1999;6:253-259.
51. Cline M, Hughey R, Karplus K. Predicting reliable regions in protein sequence alignments. Bioinformatics 2002;18:306-314.
52. Tress ML, Jones D, Valencia A. Predicting reliable regions in protein alignments from sequence profiles. J Mol Biol 2003;330:705-718.
53. Dopazo J. A new index to find regions showing an unexpected variability or conservation in sequence alignments. Comput Appl Biosci 1997;13:313-317.
54. Mevissen HT, Vingron M. Quantifying the local reliability of a sequence alignment. Protein Eng 1996;9:127-132.
55. Laskowski RA, MacArthur MW, Thornton JM. Validation of protein models derived from experiment. Curr Opin Struct Biol 1998;8:631-639.
56. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. Procheck - a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
57. Hooft RW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996;381:272.
58. Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 1993;2:1511-1519.
59. Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883.
60. 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.
61. Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006;15:2507-2524.
62. 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.
63. Rojnuckarin A, Subramaniam S. Knowledge-based interaction potentials for proteins. Proteins 1999;36:54-67.
64. Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000;10:139-145.
65. Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004;56:502-518.
66. Matsuo Y, Nishikawa K. Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci 1994;3:2055-2063.
67. Baumann G, Frommel C, Sander C. Polarity as a criterion in protein design. Protein Eng 1989;2:329-334.
68. Holm L, Sander C. Evaluation of protein models by atomic solvation preference. J Mol Biol 1992;225:93-105.
69. Gregoret LM, Cohen FE. Protein folding. Effect of packing density on chain conformation. J Mol Biol 1991;219:109-122.
70. Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. A composite score for predicting errors in protein structure models. Protein Sci 2006;15:1653-1666.
71. Wallner B, Elofsson A. Can correct protein models be identified? Protein Sci 2003;12:1073-1086.
72. Tosatto SC. The victor/FRST function for model quality estimation. J Comput Biol 2005;12:1316-1327.
73. Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999;287:797-815.
74. Lindahl E, Elofsson A. Identification of related proteins on family, superfamily and fold level. J Mol Biol 2000;295:613-25.
75. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
76. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 2002;30:264-267.
77. Zemla A. LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374.
78. Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 2005;61:127-136.
79. Stebbings LA, Mizuguchi K. HOMSTRAD: recent developments of the homologous protein structure alignment database. Nucleic Acids Res 2004;32(Database issue):D203-D207.
80. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
81. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
82. Wang G, Dunbrack RL, Jr. Scoring profile-to-profile sequence alignments. Protein Sci 2004;13:1612-1626.
83. Altschul SF, Madden TL, Schaffer 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.
84. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2005;33(Database issue):D39-D45.
85. Wootton JC. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 1994;18:269-285.
86. Adamczak R, Porollo A, Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 2005;59:467-475.
87. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-637.
88. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
89. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
90. Moult J, Fidelis K, Rost B, Hubbard T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP) - round 6. Proteins 2005;61 (Suppl):73-77.
91. Koradi R, Billeter M, Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-32.
92. Northrup SH, Pear MR, Morgan JD, McCammon JA, Karplus M. Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements. J Mol Biol 1981;153:1087-1109.