Multiple graph regularized protein domain ranking

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Wang, Jim Jing Yan ^a   Bensmail, Halima ^b   Gao, Xin ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^b QATAR COMPUTING RESEARCH INSTITUTE   (Qatar)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBAL STRUCTURE; GRAPH MODEL; INITIAL GRAPH; ITERATIVE ALGORITHM; MANIFOLD STRUCTURES; OBJECTIVE FUNCTIONS; PAIR-WISE COMPARISON; PARAMETER SELECTION; PROTEIN DOMAINS; RANKING ALGORITHM; RANKING METHODS; RANKING PERFORMANCE; SINGLE GRAPH; STRUCTURAL BIOLOGY;

ALGORITHMS; GRAPH THEORY; WEBSITES;

PROTEINS;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; METHODOLOGY; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

ALGORITHMS; DATABASES, PROTEIN; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SOFTWARE;

MLCS; MLOWN;

EID: 84869109105     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-307     Document Type: Article

References (22)

1. Zhang Y, Sun Y. HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors. BMC Bioinformatics 2011, 12:198. 10.1186/1471-2105-12-198, 3115854, 21609463.
2. Ochoa A, Llinas M, Singh M. Using context to improve protein domain identification. BMC Bioinformatics 2011, 12:90. 10.1186/1471-2105-12-90, 3090354, 21453511.
3. Zhang L, Bailey J, Konagurthu AS, Ramamohanarao K. A fast indexing approach for protein structure comparison. BMC Bioinformatics 2010, 11(Suppl 1):S46. 10.1186/1471-2105-11-S1-S46, 20122220.
4. Stivala A, Wirth A. Tableau-based protein substructure search using quadratic programming. BMC Bioinformatics 2009, 10:153. 10.1186/1471-2105-10-153, 2705363, 19450287.
5. Stivala AD, Stuckey PJ, Wirth AI. Fast and accurate protein substructure searching with simulated annealing and GPUs. BMC Bioinformatics 2010, 11:446. 10.1186/1471-2105-11-446, 2944279, 20813068.
6. Bai X, Yang X, Latecki LJ, Liu W, Tu Z. Learning Context-Sensitive Shape Similarity by Graph Transduction. IEEE Transactions on Pattern Analysis and Machine Intelligence 2010, 32(5):861-874.
7. Carpentier M, Brouillet S, Pothier J. YAKUSA: A fast structural database scanning method. Proteins-Structure Function and Bioinformatics 2005, 61(1):137-151.
8. Jung J, Lee B. Protein structure alignment using environmental profiles. Protein Engineering 2000, 13(8):535-543. 10.1093/protein/13.8.535, 10964982.
9. Lee B, Lee D. Protein comparison at the domain architecture level. BMC Bioinformatics 2009, 10(Suppl 15):S5. 10.1186/1471-2105-10-S15-S5, 2788356, 19958515.
10. Weston J, Kuang R, Leslie C, Noble W. Protein ranking by semi-supervised network propagation. BMC Bioinformatics 2006, 7(Suppl 1):S10. 10.1186/1471-2105-7-S1-S10, 1764466, 17254294.
11. Cai D, He X, Han J, Huang TS. Graph Regularized Nonnegative Matrix Factorization for Data Representation. IEEE Transactions on Pattern Analysis and Machine Intelligence 2011, 33(8):1548-1560.
12. Varma S, Simon R. Bias in error estimation when using cross-validation for model selection. BMC Bioinformatics 2006, 7:91. 10.1186/1471-2105-7-91, 1397873, 16504092.
13. Nagel K, Jimeno-Yepes A, Rebholz-Schuhmann D. Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb. BMC Bioinformatics 2009, 10(Suppl 8):S4. 10.1186/1471-2105-10-S8-S4, 2788355, 19958514.
14. Geng B, Tao D, Xu C, Yang L, Hua X. Ensemble Manifold Regularization. IEEE Transactions on Pattern Analysis and Machine Intelligence 2012, 34(6):1227-1233.
15. You ZH, Yin Z, Han K, Huang DS, Zhou X. A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. BMC Bioinformatics 2010, 11:343. 10.1186/1471-2105-11-343, 2909217, 20573270.
16. Song M, Yu H, Han WS. Combining active learning and semi-supervised learning techniques to extract protein interaction sentences. BMC Bioinformatics 2011, 12(Suppl 12):S4. 10.1186/1471-2105-12-S12-S4, 3278844, 22373238.
17. Kandaswamy KK, Pugalenthi G, Hazrati MK, Kalies KU, Martinetz T. BLProt: prediction of bioluminescent proteins based on support vector machine and relieff feature selection. BMC Bioinformatics 2011, 12:345. 10.1186/1471-2105-12-345, 3176267, 21849049.
18. Tung CW, Ziehm M, Kaemper A, Kohlbacher O, Ho SY. POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics 2011, 12:446. 10.1186/1471-2105-12-446, 3228774, 22085524.
19. Shi JY, Zhang YN. Fast SCOP classification of structural class and fold using secondary structure mining in distance matrix. Pattern Recognition in Bioinformatics. Proceedings 4th IAPR International Conference, PRIB 2009 2009, 344-53. ENGLAND: Sheffield.
20. Albatineh AN, Niewiadomska-Bugaj M. Correcting Jaccard and other similarity indices for chance agreement in cluster analysis. Advances in Data Analysis and Classification 2011, 5(3):179-200.
21. Chandonia J, Hon G, Walker N, Lo C, Koehl P, Levitt M, Brenner S. The ASTRAL Compendium in 2004. Nucleic Acids Research 2004, 32(SI):D189-D192. 308768, 14681391.
22. Kim C, Basner J, Lee B. Detecting internally symmetric protein structures. BMC Bioinformatics 2010, 11:303. 10.1186/1471-2105-11-303, 2894822, 20525292.