Fold recognition by combining profile-profile alignment and support vector machine

Bioinformatics

Volumn 21, Issue 11, 2005, Pages 2667-2673

  Han, Sangjo ^a   Lee, Byung Chul ^a   Yu, Seung Taek ^a   Jeong, Chan Seok ^a   Lee, Soyoung ^a   Kim, Dongsup ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN FOLDING; RECEIVER OPERATING CHARACTERISTIC; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE;

EID: 20744433230     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti384     Document Type: Article

References (41)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Bourne,P.E. et al. (2004) The status of structural genomics defined through the analysis of current targets and structures. Pac. Symp. Biocomput., 375-386.
3. Bowie,J.U. et al. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
4. Brenner,S.E. (2000) Target selection for structural genomics. Nat. Struct. Biol., 7 (Suppl), 967-969.
5. Chandonia,J.M. et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32 (Database issue), D189-D192.
6. Chen,L. et al. (2004) TargetDB: a target registration database for structural genomics projects. Bioinformatics, 20, 2860-2862.
7. Elofsson,A. (2002) A study on protein sequence alignment quality. Proteins, 46, 330-339.
8. Friedberg,I. et al. (2004) The interplay of fold recognition and experimental structure determination in structural genomics. Curr. Opin. Struct. Biol., 14, 307-312.
9. Gribskov,M. and Robinson,N.L. (1996) The use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem., 20, 25-34.
10. Hou,J. et al. (2003a) A global representation of the protein fold space. Proc. Natl Acad. Sci. USA, 100, 2386-2390.
11. Hou,Y. et al. (2003b) Efficient remote homology detection using local structure. Bioinformatics, 19, 2294-2301.
12. Hou,Y. et al. (2004) Remote homolog detection using local sequence-structure correlations. Proteins, 57, 518-530.
13. Hua,S. and Sun,Z. (2001) A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach. J. Mol. Biol., 308, 397-407.
14. Jaakkola,T. et al. (2000) A discriminative framework for detecting remote protein homologies. J. Comput. Biol., 7, 95-114.
15. Jones,D.T. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol., 287, 797-815.
16. Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
17. Karplus,K. et al. (1999) Predicting protein structure using only sequence information. Proteins, (Suppl 3), 121-125.
18. Kelley,L.A. et al. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol., 299, 499-520.
19. Kim,D. et al. (2003) PROSPECT II: protein structure prediction program for genome-scale applications. Protein Eng., 16, 641-650.
20. Kim,S.H. (1998) Shining a light on structural genomics. Nat. Struct. Biol., 5 (Suppl), 643-645.
21. Kinch,L.N. et al. (2003) CASP5 assessment of fold recognition target predictions. Proteins, 53 (Suppl 6), 395-409.
22. Liao,L. and Noble,W.S. (2003) Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J. Comput. Biol., 10, 857-868.
23. McGuffin,L.J. et al. (2004) The genomic threading database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Res., 32 (Database issue), D196-D199.
24. Murzin,A.G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
25. Ohlson,T. et al. (2004) Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins, 57, 188-197.
26. Park,J. et al. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
27. Platt,J.C. (1999) Probabilistic outputs for support vector machines and comparisons to regularized likehood methods. In Smola,A., Bartlett,P., Scholkopf,D. and Schuurmans,D. (eds), Advances in Large Margin Classifiers. MIT Press, Cambridge, MA, pp. 61-74.
28. Przybylski,D. and Rost,B. (2004) Improving fold recognition without folds. J. Mol. Biol., 341, 255-269.
29. Qian,J. et al. (2001 ) Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J. Mol. Biol., 313, 673-681.
30. Rychlewski,L. et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
31. Rychlewski,L. et al. (2003) LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins, 53 (Suppl 6), 542-547.
32. Sadreyev,R. and Grishin,N. (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
33. Shi,J. et al. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243-257.
34. Tress,M.L. et al. (2003) Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol., 330, 705-718.
35. Vapnik,V. (1998) Statistical Learning Theory. Wiley, New York.
36. Von Ohsen,N. et al. (2004) Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics, 20, 2228-2235.
37. Wallner,B. et al. (2004) Using evolutionary information for the query and target improves fold recognition. Proteins, 54, 342-350.
38. Weston,J. et al. (2004) Protein ranking: from local to global structure in the protein similarity network. Proc. Natl Acad. Sci. USA, 101, 6559-6563.
39. Xu,J. et al. (2003) RAPTOR: optimal protein threading by linear programming. J. Bioinform. Comp. Biol., 1, 95-117.
40. Xu,Y. and Xu,D. (2000) Protein threading using PROSPECT: design and evaluation. Proteins, 40, 343-354.
41. Yona,G. and Levitt,M. (2002) Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.