Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence

Proteins: Structure, Function and Genetics

Volumn 49, Issue 2, 2002, Pages 154-166

  Kloczkowski, A ^a   Ting, K L ^a   Jernigan, R L ^a,c   Garnier, J ^b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c IOWA STATE UNIVERSITY   (United States)

Author keywords

GOR algorithm; Information theory; Multiple sequence alignment; Protein secondary structure; PSI BLAST; Secondary structure prediction

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DATA BASE; GOR V ALGORITHM; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; ONLINE ANALYSIS; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICS;

ALGORITHMS; ANIMALS; EVOLUTION, MOLECULAR; INFORMATION THEORY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 0036836642     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10181     Document Type: Article

References (51)

1. Kabsch W, Sander C. A dictionary of protein secondary structure. Biopolymers 1983;22:2577-2637.
2. The address of the FTP server for the DSSP assignments for chains from the PDB is ftp://ftp.embl-heidelberg.de/pub/databases/dssp.
3. Rost B, Sander C. Third generation prediction of secondary structure. In: Webster DM, editor. Protein structure prediction: methods and protocols. Totowa, NJ: Humana Press; 2000. p 71-95.
4. Moult J, Judson R, Fidelis K, Pedersen JT. A large scale experiment to assess protein structure prediction. Proteins 1995;23:I-IV.
5. Frishman D, Argos P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins 1997;27:329-335.
6. Biou V, Gibrat JF, Levin J, Robson B, Garnier J. Secondary structure prediction: combination of three different methods. Protein Eng 1988;2:185-191.
7. Salamov AA, Solovyev VV. Prediction of protein secondary structure by combining nearest-neighbor algorithm and multiple sequence alignments. J Mol Biol 1995;247:11-15.
8. 4 phage lysozyme. Biochim Biophys Acta 1975; 405:442-451.
9. Zemla A, Venclovas C, Fidelis K, Rost B. A modified definition of Sov, a segment-based measure of protein secondary structure prediction assessment. Proteins 1999;34:220-223.
10. Rost B, Sander C, Schneider R. Redefining the goals of protein secondary structure prediction. J Mol Biol 1994;235:13-26.
11. Chou PY, Fasman GD. Prediction of protein conformation. Biochemistry 1974;13:211-215.
12. Lim VI. Structural principles of the globular organization of protein chains: a stereochemical theory of globular protein secondary structure. J Mol Biol 1974;88:857-872.
13. Lim VI. Algorithm for prediction of α-helical and β-structural regions in globular proteins. J Mol Biol 1974;88:873-894.
14. Garnier 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.
15. Gibrat JF, Garnier J, Robson B. Further developments of protein secondary structure prediction using information theory: new parameters and consideration of residue pairs. J Mol Biol 1987;198: 425-443.
16. Garnier J, Robson B. The GOR method for predicting secondary structures in proteins. In: Fasman GD, editor. Prediction of protein structure and the principles of protein conformation. New York: Plenum Press; 1989. p 417-465.
17. Garnier J, Gibrat JF, Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 1996;266:540-553.
18. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
19. Rost B, Sander C, Schneider R. PHD: an automatic mail server for protein secondary structure prediction. Comput Appl Biosci 1994; 10:53-60.
20. Holley LH, Karplus M. Protein secondary structure prediction with a neural network. Proc Natl Acad Sci USA 1989;86:152-156.
21. Qian N, Sejnowski TJ. Predicting the secondary structure of a globular proteins using neural network models. J Mol Biol 1989; 202:865-884.
22. Stolorz P, Lapedes A, Xia Y. Predicting protein secondary structure using neural net and statistical methods. J Mol Biol 1992;225: 1049-1063.
23. Petersen TN, Lundegaard C, Nielsen M, et al. Prediction of protein secondary structure at 80% accuracy. Proteins 2000;41:17-20.
24. Jones TD. Protein secondary structure prediction based on position specific scoring matrices. J Mol Biol 1999;292:195-202.
25. Levin JM, Robson B, Garnier J. An algorithm for secondary structure determination in proteins based on sequence similarity. FEBS Lett 1986;205:303-308.
26. Levin JM, Garnier J. Improvements in secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool. Biochim Biophys Acta 1988;955: 283-295.
27. Salamov AA, Solovyev VV. Protein secondary structure prediction using local alignments. J Mol Biol 1997;268:31-36.
28. Yi T-M, Lander ES. Protein secondary structure prediction using nearest-neighbor methods. J Mol Biol 1993;232:1117-1129.
29. Salzberg S, Cost S. Predicting protein secondary structure with nearest-neighbors algorithm. J Mol Biol 1992;227:371-374.
30. Cuff JA, Barton GJ. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 1999;34:508-519.
31. Cuff JA, Barton GJ. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000;40:502-511.
32. King RD, Sternberg MJ. Machine learning approach for prediction of protein secondary structure. J Mol Biol 1990;216:441-457.
33. Barton GJ. Protein secondary structure prediction. Curr Opin Struct Biol 1995;5:372-376.
34. Karplus K, Barrett C, Hughley R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
35. Ouali M, King RD. Cascaded multiple classifiers for secondary structure prediction. Protein Sci 2000;9:1162-1176.
36. Rost B. Review: protein secondary structure prediction continues to rise. J Struct Biol 2001;134:204-218.
37. Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJE. Prediction of protein secondary structure and active sites using alignment of homologous sequences. J Mol Biol 1987;195:957-961.
38. Levin JM, Pascarella S, Argos P, Garnier J. Quantification of secondary structure prediction improvement using distantly related proteins. Protein Eng 1993;6:849-854.
39. Rost B. PHD: predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol 1996;266:525-539.
40. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
41. Di Francesco V, Garnier J, Munson PJ. Improving protein secondary structure prediction with aligned homologous sequences. Protein Sci 1996;5:106-113.
42. Russell RB, Barton GJ. The limits of protein secondary structure prediction accuracy from multiple sequence alignment. J Mol Biol 1993;234:951-957.
43. Lecompte O, Thompson JD, Plewniak F, Thierry JC, Poch O. Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene 2001;270:17-30.
44. Kloczkowski A, Ting K-L, Jernigan RL, Garnier J. Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information. Polymer 2002;43: 441-449.
45. Rost B, Eyrich VA, Przybylski D, et al. EVA: evaluation of automatic protein structure prediction services. www.http://cubic.bioc.columbia.edu/eva.
46. Rychlewski L, Fischer D. LiveBench: continuous benchmarking of prediction servers. www.http://bioinfo.pl/LiveBench.
47. Zhang CT, Chou KC. An optimization approach to predicting protein structural class from amino acid composition. Protein Sci 1992;1:401-408.
48. Chou KC. Does the folding type of protein depend on its amino acid composition? FEBS Lett 1995;363:127-131.
49. Eisenhaber F, Imperiale F, Argos P, Frommel C. Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods. Proteins 1996;25:157-168.
50. Eisenhaber F, Frommel C, Argos P. Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class. Proteins 1996;25:169-179.
51. Bahar I, Altigan AR, Jernigan R, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins 1997;29:172-185.