Combining classifiers for improved classification of proteins from sequence or structure

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Melvin, Iain ^a   Weston, Jason ^a   Leslie, Christina S ^b   Noble, William S ^c  

^a NEC LABORATORIES AMERICA   (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; COMBINING CLASSIFIERS; COMPUTATIONAL BIOLOGY; DISCRIMINATIVE LEARNING; HYBRID MACHINE LEARNING; INDIVIDUAL COMPONENTS; NEAREST NEIGHBOR METHOD; SUPPORT VECTOR MACHINE (SVMS);

AMINO ACIDS; BIOINFORMATICS; LEARNING ALGORITHMS; SUPPORT VECTOR MACHINES;

PROTEINS;

PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; LEARNING ALGORITHM; MACHINE LEARNING; PREDICTION; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SUPPORT VECTOR MACHINE; ALGORITHM; CHEMISTRY; CLASSIFICATION; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; SYSTEM ANALYSIS; ULTRASTRUCTURE;

ALGORITHMS; AMINO ACID SEQUENCE; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP; SYSTEMS INTEGRATION;

EID: 53349096696     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-389     Document Type: Article

References (21)

1. Shindyalov IN Bourne PE Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Engineering 1998, 11:739-747. 10.1093/protein/11.9.739 9796821
2. Holm L Sander C Protein Structure Comparison by Alignment of Distance Matrices Journal of Molecular Biology 1993, 233:123-138. 10.1006/ jmbi.1993.1489 8377180
3. Ortiz AR Strauss CEM Olmea O MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison Protein Science 2002, 11:2606-2621. 2373724 12381844 10.1110/ps.0215902
4. Smith T Waterman M Identification of common molecular subsequences Journal of Molecular Biology 1981, 147:195-197. 10.1016/ 0022-2836(81)90087-5 7265238
5. Altschul SF Gish W Miller W Myers EW Lipman DJ A basic local alignment search tool Journal of Molecular Biology 1990, 215:403-410. 2231712
6. Karplus K Barrett C Hughey R Hidden Markov models for detecting remote protein homologies Bioinformatics 1998, 14(10):846-56. 10.1093/ bioinformatics/14.10.846 9927713
7. 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 Research 1997, 25:3389-3402. 146917 9254694 10.1093/nar/25.17.3389
8. Jaakkola T Diekhans M Haussler D Using the Fisher kernel method to detect remote protein homologies Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology Menlo Park, CA: AAAI Press 1999, 149-158.
9. Boser BE Guyon IM Vapnik VN A Training Algorithm for Optimal Margin Classifiers 5th Annual ACM Workshop on COLT Pittsburgh, PA: ACM Press Haussler D 1992, 144-152.
10. Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures Journal of Molecular Biology 1995, 247:536-540. 7723011
11. Noble WS Support vector machine applications in computational biology Kernel methods in computational biology Cambridge, MA: MIT Press Schoelkopf B, Tsuda K, Vert JP 2004, 71-92.
12. Melvin I Ie E Kuang R Weston J Noble WS Leslie C SVM-fold: A tool for discriminative multi-class protein fold and superfamily recognition BMC Bioinformatics 2007, 8(Suppl 4):S2. 1892081 17570145 10.1186/ 1471-2105-8-S4-S2
13. Melvin I Ie E Weston J Noble WS Leslie C Multi-class protein classification using adaptive codes Journal of Machine Learning Research 2007, 8:1557-1581.
14. Rangwala H Karypis G Building multiclass classifiers for remote homology detection and fold recognition BMC Bioinformatics 2006, 16(7):455. 17042943 10.1186/1471-2105-7-455
15. Shamim MT Anwaruddin M Nagarajaram HA Support vector machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs Bioinformatics 2007, 23(24):3320-3327. 10.1093/bioinformatics/btm527 17989092
16. Kuang R Ie E Wang K Wang K Siddiqi M Freund Y Leslie C Profile-based string kernels for remote homology detection and motif extraction Journal of Bioinformatics and Computational Biology 2005, 3(3):527-550. 16108083 10.1142/S021972000500120X
17. Dobson PD Doig AJ Predicting Enzyme Class From Protein Structure Without Alignments Journal of Molecular Biology 2005, 345:187-199. 10.1016/ j.jmb.2004.10.024 15567421
18. Borgwardt K Ong CS Schoenauer S Vishwanathan S Smola A Kriegel HP Protein Function Prediction via Graph Kernels Bioinformatics 2005, 21(Suppl 1):i47-i56. 10.1093/bioinformatics/bti1007 15961493
19. Qiu J Hue M Ben-Hur A Vert JP Noble WS A structural alignment kernel for protein structures Bioinformatics 2007, 23(9):1090-1098. 10.1093/ bioinformatics/btl642 17234638
20. Wolpert D Stacked generalization Neural Networks 1992, 5(2):241-259. 10.1016/S0893-6080(05)80023-1
21. Jan E Gewehr VH Zimmer R AutoSCOP: Automated Prediction of SCOP Classifications using Unique Pattern-Class Mappings Bioinformatics 2007, 23(10):1203-1210. 10.1093/bioinformatics/btm089 17379694