Prediction of binding sites in HCV protein complexes using a support vector machine

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5226 LNCS, Issue , 2008, Pages 130-137

  Yoo, Taihui ^a   Lee, Jaetak ^a   Han, Kyungsook ^a  

^a Inha University   (South Korea)

Author keywords

Binding sites; Hepatitis C virus; Support vector machine

Indexed keywords

BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; FLOW INTERACTIONS; FORECASTING; HEALTH RISKS; HYPERSONIC AERODYNAMICS; IMAGE RETRIEVAL; LEARNING SYSTEMS; PROTEINS; VECTORS; VIRUSES;

AVERAGE SENSITIVITIES; BINDING RESIDUES; HEPATITIS C VIRUS; HEPATITIS C VIRUSES; HUMAN PROTEINS; LIVER DISEASES; POTENTIAL PROTEINS; PROTEIN COMPLEXES; PROTEIN INTERACTIONS; PUBLIC HEALTHS; SUPPORT VECTOR MACHINE; SUPPORT VECTORS; SVM MODELS;

SUPPORT VECTOR MACHINES;

EID: 56549125841     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-87442-3_18     Document Type: Conference Paper

References (16)

1. Bogen, S., Saksena, A.K., Arasappan, A., Gu, H., Njoroge, F.G., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Prongay, A., Madison, V.: Hepatitis C Virus NS3-4A Serine Protease Inhibitors: Use of a P2-P1 Cyclopropyl Alanine Combination for Improved Potency. Bioorg. Med. Chem. Lett. 15, 4515-4519 (2005)
2. Powers, J.P., Piper, D.E., Li, Y., Mayorga, V., Anzola, J., Chen, J.M., Jaen, J.C., Lee, G., Liu, J., Peterson, M.G., Tonn, G.R., Ye, Q., Walker, N.P., Wang, Z.: SAR and Mode of Action of Novel Non-nucleoside Inhibitors of Hepatitis C NS5b RNA Polymerase. J. Med. Chem. 49, 1034-1046 (2006)
3. Hsu, E.C., His, B., Hirota-Tsuchihara, M., Rulan, J., Iorio, C., Sarangi, F., Diao, J., Migliaccio, G., Tyrrell, D.L., Kneteman, N., Richardson, C.D.: Modified Apoptotic Molecule (BID) Reduces Hepatitis C Virus Infection in Mice with Chimeric Human Livers. Nat. Biotechnol. 21, 519-525 (2003)
4. Evans, M.J., Rice, CM., Goff, S.P.: Phosphorylation of Hepatitis C Virus Nonstructural Protein 5A Modulates Its Protein Interactions and Viral RNA Replication. Proc. Natl. Acad. Sci. 101, 13038-13043 (2004)
5. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucl. Acids. Res. 28, 235-242 (2000)
6. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucl. Acids. Res. 25, 3389-3402 (1997)
7. Zhang, G.Z., Nepal, C., Han, K.: Predicting Binding Sites of Hepatitis C Virus Complexes Using Residue Binding Propensity and Sequence Entropy. In: Shi, Y., van Albada, G.D., Dongarra, J., Sloot, P.M.A. (eds.) ICCS 2007. LNCS, vol. 4487, pp. 78-85. Springer, Heidelberg (2007)
8. Sander, C., Schneider, R.: Database of Homology-derived Protein Structures and the Structural Meaning of Sequence Alignment. Proteins 9, 56-58 (1991)
9. Homology-derived Secondary Structure of Proteins, http://swift.cmbi.kun. nl/gv/hssp
10. Dodge, C., Schneider, R., Sander, C.: The HSSP Database of Protein Structure-sequence Alignments and Family Profiles. Nucl. Acids. Res. 26, 313-315 (1998)
11. Jones, S., Thornton, J.M.: Analysis of Protein-protein Interaction Sites Using Surface Patches. J. Mol. Biol. 272, 121-132 (1997)
12. 2: Protein-protein Interaction Predictions Using Patch Analysis. Bioinformatics 22, 1794-1795 (2006)
13. Jones, S., Thornton, J.M.: Prediction of Protein-Protein Interaction Sites Using Patch Analysis. J. Mol. Biol. 272, 133-143 (1997)
14. Efron, B., Tibshirani, R.J.: An Introduction to the Bootstrap. Chapman and Hall, London (1993)
15. Georges, D., Masato, K.: Bootstrap Re-sampling for Unbalanced Data in Supervised Learning. Eur. J. Oper. Res. 134, 141-156 (2001)
16. Zweig, M.H., Campbell, G: Receiver-operating Characteristic (ROC) Plots: A Fundamental Evaluation Tool in Clinical Medicine. Clin. Chem. 39, 561-577 (1993)