Evaluation and improvement of multiple sequence methods for protein secondary structure prediction

Proteins: Structure, Function and Genetics

Volumn 34, Issue 4, 1999, Pages 508-519

  Cuff, James A ^a,b   Barton, Geoffrey J ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Benchmarks; Combination of methods; Protein; Secondary structure prediction

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE;

ALGORITHMS; COMPUTER SIMULATION; DATABASES, FACTUAL; MODELS, STATISTICAL; PROTEIN STRUCTURE, SECONDARY; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT;

EID: 0033106244     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990301)34:4<508::AID-PROT10>3.0.CO;2-4     Document Type: Article

References (84)

1. Sail A. Modelling mutations and homologous proteins. Curr Opin Biotechnol 1995; 6:437-451.
2. Brenner SE, Chothia C, Hubbard TJP. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci 1998;95:6073-6078.
3. Taylor WR. Identification of protein sequence homology by consensus template alignment. J Mol Biol 1986;188:233-258.
4. Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci 1987;84:4355-4358.
5. Barton GJ. Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol 1990;183:403-428.
6. Barton GJ, Sternberg MJE. A strategy for the rapid multiple alignment of protein sequences: confidence levels from tertiary structure comparisons. J Mol Biol 1987;198:327-337.
7. Eddy SR. Hidden markov models. Curr Opin Struct Biol 1996;6: 361-365.
8. Karplus K, Sjolander K, Barrett C, et al. Predicting protein structure using hidden markov models. Proteins 1997; Suppl 1:134-139.
9. Park J, Teichmann SA, Hubbard T, Chothia C. Intermediate sequences increase the detection of distant sequence homologues. J Mol Biol 1997;273:349-354.
10. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
11. Lemer C, Rooman MJ, Wodak SJ. Protein structure prediction by threading methods: evaluation of current techniques. Proteins 1996;23:337-355.
12. Russell RB, Barton GJ. An SH2-SH3 domain hybrid. Nature 1993;364:765-765.
13. Russell RB, Copley RR, Barton GJ. Protein fold recognition by mapping predicted secondary structures. J Mol Biol 1996;259:349-365.
14. Rost B. TOPITS: threading one-dimensional preditions into three-dimensional structures. Proceedings from the Third International Conference on Intelligent Systems for Molecular Biology. Menlo Park, CA: AAA1 Press, 1995. p 314-321.
15. Rost B. Protein fold recognition by prediction-based threading. J Mol Biol 1997;270:1-10.
16. Lim VI. Algorithms for prediction of α helices and β structural regions in globular proteins. J Mol Biol 1974;88:873-894.
17. Chou PY, Fasman GD. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry 1974;13:211-222.
18. Gamier J, Osguthorpe DJ, Robson B. Analysis and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978;120:97-120.
19. Schulz GE, Schirmer RH. Principles of Proteins Structure. New York: Springer-Verlag, 1979. p 1-314.
20. Kabsch W, Sander C. How good are predictions of protein secondary structure? FEES Lett 1983;155:179-182.
21. Livingstone CD, Barton GJ. Identification of functional residues and secondary structure from protein multiple sequence alignment. Methods Enzymol 1996;266:497-512.
22. Crawford IP, Niermann T, Kirchner K. Prediction of secondary structure by evolutionary comparison: application to the alpha subunit of tryptophan synthase. Proteins 1987;2:118-129.
23. Barton GJ, Newman RH, Freemont PF, Crumpton MJ. Amino acid sequence analysis of the annexin super-gene family of proteins. Eur J Biochem 1991;198:749-760.
24. Russell RB, Breed J, Barton GJ. Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains. FEBS Lett 1992;304:15-20.
25. Benner SA, Gerloff D. Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases. Adv Enzyme Regul 1990;31:121-181.
26. Zvelebil MJJM, Barton GJ, Taylor WR, Sternberg MJE. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J Mol Biol 1987;195:957-961.
27. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
28. Frishman D, Argos P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins 1997;27:329-335.
29. King RD, Sternberg MJE. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci 1996;5:2298-2310.
30. Salamov AA, Solovyev W. Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J Mol Biol 1995;247:11-15.
31. Proteins 1997; Suppl 1:1-230.
32. Rost B. Better ID predictions by experts with machines. Proteins 1997; Suppl 1:192-197.
33. Biou V, Gilbrat JF, Robson B, Garnier J. Secondary structure prediction: combination of three different methods. Protein Eng 1995;2:185-191.
34. Zhang X, Mesriov D, Waltz J. A hybrid system for protein secondary structure prediction. J Mol Biol 1992;225:1049-1063.
35. Nishikawa K, Ooi T. Amino acid sequence homology applied to the prediction of protein secondary structures, and joint prediction with existing methods. Biochim Biophys Acta 1986;871:45-54.
36. Nishikawa K, Nogughi T. Predicting protein secondary structure based on amino acid sequence. Methods Enzymol 1995;202:31-44.
37. Geourjon C, Deleage G. Sopma: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 1995;11:681-684.
38. Kabsch W, Sander C. A dictionary of protein secondary structure. Biopolymers 1983;22:2577-2637.
39. Richards FM, Kundrot CE. Identification of structural motifs from protein coordinate data: secondary structure and first-level super-secondary structure. Proteins 1988;3:71-84.
40. Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
41. Boscott PE, Barton GJ, Richards WG. Secondary structure prediction for modelling by homology. Protein Eng 1993;6:261-266.
42. Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 1991;9:56-68.
43. Feng DF, Johnson MS, Doolittle RF. Aligning amino acid sequences: comparison of commonly used methods. J Mol Evol 1985;21:112-125.
44. 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.
45. Siddiqui A, Barton GJ. 3Dee - database of protein domain definitions. 1998; submitted.
46. Barton GJ, Sternberg MJ. Evaluation and improvements in the automatic alignment of protein sequences. Protein Eng 1987;1: 89-94.
47. Murzin A, Brenner SE, Hubbard T, Chothia C. Scop: a structural classification of proteins database and the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
48. Newman M, Frazao C, Khan G, Tickle IJ, Blundell TL, Safro M, Andreeva N, Zdanov A. X-ray analyses of aspartic proteinases. Structure and refinement at 2.2 angstroms resolution of bovine chymosin. J Mol Biol 1991;221:1295-1309.
49. Sali A, Veerapandian B, Cooper JB, Foundling SI, Hoover DJ, Blundell TL. High resolution x-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor. The analysis of the inhibitor binding and description of the rigid body shift in the enzyme. EMBO J 1989;8:2179-2188.
50. Satow Y, Cohen GH, Padlan EA, Davies DR. Phosphocholine binding immunoglobulin study at 2.7 angstroms. J Mol Biol 1987;190:593-604.
51. Bolognesi M, Gatti G, Menegatti E, et al. Three dimensional structure of the complex between pancreatic secretory inhibitor (kazal type) and trypsinogen at 1.8 angstroms resolution. J Mol Biol 1982;162:839-868.
52. Honzatko RB, Hendrickson WA, Love WE. Refinement of a molecular model for lamprey hemoglobin from perromyzon marinus. J Mol Biol 1985;184:147-164.
53. Garrett TPJ, Guss JM, Freeman HC. The crystal structure of poplar apoplastocyanin at 1.8 Angstroms resolution. J Biol Chem 1984;259:2822-2825.
54. Smith JL, Corfields PWR, Hendrickson WA, Low BW. Refinement at 1.4 angstroms resolution of a model of erabutoxin B. Treatment of ordered olvent and discrete order. Acta Crystallogr Sect A 1988;44:357-362.
55. Kumar VD, Lee L, Edwards BFP. Refined crystal structure of calcium liganded carp paravalbumin 4.25 at 1.5 angstroms resolution. Biochemistry 1990;29:1404-1412.
56. Fitzgerald PMD, Mc Keever BM, Van Middlesworth JF, Springer JP. Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl pepstatin at 2.0 angstroms resolution. J Biol Chem 1990;265:14209-14219.
57. Quiocho FA, Wilson DK, Vyas NK. Substrate specificity and affinity of a protein modulated by bound water molecules. Nature 1989;340:404-407.
58. Frishman D, Argos P. Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng 1996;9:133-142.
59. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
60. Bleasby AJ, Akrigg D, Attwood TK. OWL - a non-redundant, composite protein sequence database. Nucleic Acids Res 1994;22: 3574-3577.
61. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
62. Barton GJ. Alscript: a tool to format multiple sequence alignments. Protein Eng 1993;6:37-40.
63. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sesitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weigh matrix choice. Nucleic Acids Res 1994;22:4673-4680.
64. Rost BR, Sander C, Schneider R. Redefining the goals of protein secondary structure prediction. J Mol Biol 1994;235:13-26.
65. Reference deleted in proofs.
66. Bowie JU, Luthy R, Eisnenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
67. Huang X, Miller WA. A time efficient, linear-space local similarity algorithm. Adv Appl Math 1991;12:337-357.
68. Taylor WR. Classification of amino acid conservation. J Theor Biol 1986;119:205-218.
69. Rose GD. Prediction of chain turns in globular proteins on a hydrophobic basis. Nature 1978;272:586-591.
70. Wilmot ACM, Thornton JM. Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol 1988:203:221-232.
71. Sklenar H, Etchebest C, Lavery R. Describing protein structure - a general algorithm yielding complete helicoidal parameters and unique overall axis. Proteins 1989;6:46-60.
72. Levin JM. Exploring the limits of nearest neighbour secondary structure prediction. Protein Eng 1997;10:771-776.
73. Geourjon C, Deleage G. SOPM: a self optimised method for protein secondary structure prediction. Protein Eng 1994;7:157-164.
74. Robson B, Gamier J, Gibrat J. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 1996;266:540-553.
75. Steigemann W, Webber E. Structure of Erythrocruorin in different ligand states refined at 1.4 Angstroms resolution. J Mol Biol 1979;127:309-338.
76. Adman ET, Sieker LC, Jensen LH. Structural features of Azurin at 2.7 Angstroms. Isr J Chem 1981;21:8-11.
77. Wlodawer A, Miller M, Jaskolski M. Crystal structure of a retroviral protease proves relationship to aspartic protease family. Nature 1989;337:576-579.
78. Petratos K, Dauter Z, Wilson KS. Refinement of the structure of Pseudoazurin from Alcaligenes Faecalis S-6 at 1.55 Angstroms. Acta Crystallogr Sect B. 1988;44:628-636.
79. Royer WE. Jr. High resolution crystallographic analysis of a cooperative dimeric Haemoglobin. J Mol Biol 1994;657:657-681.
80. Rees B, Bilwes A, Samama JP, Moras D. Cardiotoxin from Naja Mossanmica: the refined crystal structure. J Mol Biol 1990;214: 281-297.
81. Babu YS, Bugg CE, Cook WJ. Structure of Calmodulin refined at 2.2 Angstroms resolution. J Mol Biol 1988;204:191-204.
82. Vyas NK, Vyas MN, Quiocho FA. Sugar and signal transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 1988;242:1290-1295.
83. Weber E, Papamokos E, Bode W, Huber R, Kato I, Laskowski M. Ovomucoid, a Kazal-type inhibitor, and model building studies of complexes with serine proteases. J Mol Biol 1982;158: 515-537.
84. Fischmann TO, Poljak RJ. Crystallographic refinement of the three-dimensional structure of FAB D1.2 Lysozyme complex at 2.5 Angstroms. J Biol Chem 1991;266:12915-12920.