A simple and fast secondary structure prediction method using hidden neural networks

Bioinformatics

Volumn 21, Issue 2, 2005, Pages 152-159

  Lin, Kuang ^a   Simossis, Victor A ^b   Taylor, William R ^a   Heringa, Jaap ^b  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; INFORMATION PROCESSING; INTERMETHOD COMPARISON; INTERNET; ONLINE SYSTEM; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN SECONDARY STRUCTURE; RELIABILITY; SCORING SYSTEM; STRUCTURE ANALYSIS;

EID: 13444266488     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth487     Document Type: Article

References (33)

1. Albrecht,M., Tosatto,S.C., Lengauer,T. and Valle,G. (2003) Simple consensus procedures are effective and sufficient in secondary structure prediction. Protein Eng., 16, 459-462.
2. Altschul,S.F. and Koonin,E.V. (1998) Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem. Sci., 23, 444-447.
3. 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.
4. Bishop,C.M. (1995) Neural Networks for Pattern Recognition Clarendon Press, Oxford University Press, Oxford.
5. Brenner,S.E., Koehl,P. and Levitt,M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
6. Bystroff,C. and Baker,D. (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol., 281, 565-577.
7. Bystroff,C., Thorsson,V. and Baker,D. (2000) HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J. Mol. Biol., 301, 173-190.
8. Cuff,J.A. and Barton,G.J. (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins, 40, 502-511.
9. Durbin,R. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
10. Eyrich,V.A., Przybylski,D., Koh,I.Y., Grana,O., Pazos,F., Valencia,A. and Rost,B. (2003) CAFASP3 in the spotlight of EVA. Proteins, 53 (Suppl. 6), 548-560.
11. 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 (Suppl. 6), 503-516.
12. Han,K.F. and Baker,D. (1996) Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc. Natl Acad. Sci., USA, 93, 5814-5818.
13. Heringa,J. (2000) Computational methods for protein secondary structure prediction using multiple sequence alignments. Curr. Protein Pept. Sci., 1, 273-301.
14. Hubbard,T.J., Ailey,B., Brenner,S.E., Murzin,A.G. and Chothia,C. (1998) SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallogr. D Biol. Crystallogr., 54, 1147-1154.
15. Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292 195-202.
16. Jones,D.T. and Swindells,M.B. (2002) Getting the most from PSI-BLAST. Trends Biochem Sci., 27, 161-164.
17. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
18. Karchin,R., Cline,M., Mandel-Gutfreund,Y. and Karplus,K. (2003) Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins, 51, 504-514.
19. Koh,I.Y, Eyrich,V.A., Marti-Renom,M.A., Przybylski,D., Madhusudhan,M.S., Eswar,N., Grana,O., Pazos,F., Valencia,A., Sali,A. and Rost,B. (2003) EVA: evaluation of protein structure prediction servers. Nucleic Acids Res., 31, 3311-3315.
20. Krogh,A. and Riis,S.K. (1999) Hidden neural networks. Neural Comput., 11, 541-563.
21. Martelli,P.L., Fariselli,P., Malaguti,L. and Casadio,R. (2002) Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks. Protein Eng., 15, 951-953.
22. McGuffin,L.J. and Jones,D.T. (2003) Benchmarking secondary structure prediction for fold recognition. Proteins, 52, 166-175.
23. 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.
24. Ouali,M. and King,R.D. (2000) Cascaded multiple classifiers for secondary structure prediction. Protein Sci., 9, 1162-1176.
25. Pollastri,G., Przybylski,D., Rost,B. and Baldi,P. (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47, 228-235.
26. Przybylski,D. and Rost,B. (2002) Alignments grow, secondary structure prediction improves. Proteins, 46, 197-205.
27. Qian,N. and Sejnowski,T.J. (1988) Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol., 202, 865-884.
28. Richardson,J.S. and Richardson,D.C. (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science, 240, 1648-1652.
29. Rost,B. (2001) Review: protein secondary structure prediction continues to rise. J. Struct. Biol., 134, 204-218.
30. Rost,B. and Sander,C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
31. Serrano,L. and Fersht,A.R. (1989) Capping and alpha-helix stability. Nature, 342, 296-299.
32. Simossis,V.A. and Heringa,J. (2004) Integrating secondary structure prediction and multiple sequence alignment. Curr. Protein Pept. Sci., 5, 1-15.
33. Zemla,A., Venclovas,C., Fidelis,K. and Rost,B. (1999) A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment. Proteins, 34, 220-223.