A nearest neighbor algorithm based predictor for the prediction of enzyme-small molecule interaction

Protein and Peptide Letters

Volumn 19, Issue 1, 2012, Pages 91-98

  Hu, Le Le ^a   He, Zhi Song ^b,c   Shi, Xiao He ^d   Kong, Xiang Ying ^d,e   Li, Hai Peng ^a,d   Lu, Wen Cong ^a  

^a SHANGHAI UNIVERSITY   (China)

^b Chinese Academy of Sciences   (China)

^c FUDAN UNIVERSITY   (China)

^d SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^e SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

Biochemical and physicochemical description of proteins; Chemical functional group; Feature selection; Forward feature selection; Incremental feature selection; Minimum redundancy maximum relevance

Indexed keywords

ARTICLE; COMPUTER PREDICTION; CONTROLLED STUDY; FORWARD FEATURE SELECTION; INCREMENTAL FEATURE SELECTION; INFORMATION PROCESSING; JACKKNIFE TEST; MACHINE LEARNING; MINIMUM REDUNDANCY MAXIMUM RELEVANCE; MOLECULAR INTERACTION; MOLECULAR MODEL; NEAREST NEIGHBOR ALGORITHM; PHYSICAL CHEMISTRY; PHYSICOCHEMICAL MODEL; PROTEIN FUNCTION; PROTEIN INTERACTION; REDUNDANCY ANALYSIS;

EID: 84863287185     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986612798472938     Document Type: Article

References (35)

1. Freyer, M.W.; Lewis, E.A. Isothermal titration calorimetry: experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions. Methods Cell Biol., 2008, 84, 79-113.
2. Niu, B.; Jin, Y.; Lu, L.; Fen, K.; Gu, L.; He, Z.; Lu, W.; Li, Y.; Cai, Y. Prediction of interaction between small molecule and enzyme using AdaBoost. Mol. Divers., 2009, 13(3), 313-320.
3. Weber, P.C.; Salemme, F.R. Applications of calorimetric methods to drug discovery and the study of protein interactions. Curr. Opin. Struct. Biol., 2003, 13(1), 115-121. (Pubitemid 36170263)
4. Brooksbank, C.; Cameron, G.; Thornton, J. The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Res., 2005, 33(Database issue), D46-53. (Pubitemid 40207829)
5. Caspi, R.; Foerster, H.; Fulcher, C.A.; Hopkinson, R.; Ingraham, J.; Kaipa, P.; Krummenacker, M.; Paley, S.; Pick, J.; Rhee, S.Y.; Tissier, C.; Zhang, P.; Karp, P.D. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res., 2006, 34(Database issue), D511-516.
6. Kuhn, M.; von Mering, C.; Campillos, M.; Jensen, L.J.; Bork, P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res., 2008, 36(Database issue), D684-688. (Pubitemid 351149807)
7. Wheeler, D.L.; Barrett, T.; Benson, D.A.; Bryant, S.H.; Canese, K.; Chetvernin, V.; Church, D.M.; DiCuccio, M.; Edgar, R.; Federhen, S.; Geer, L.Y.; Kapustin, Y.; Khovayko, O.; Landsman, D.; Lipman, D.J.; Madden, T.L.; Maglott, D.R.; Ostell, J.; Miller, V.; Pruitt, K.D.; Schuler, G.D.; Sequeira, E.; Sherry, S.T.; Sirotkin, K.; Souvorov, A.; Starchenko, G.; Tatusov, R.L.; Tatusova, T.A.; Wagner, L.; Yaschenko, E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 2007, 35(Database issue), D5-12.
8. Wishart, D.S.; Tzur, D.; Knox, C.; Eisner, R.; Guo, A.C.; Young, N.; Cheng, D.; Jewell, K.; Arndt, D.; Sawhney, S.; Fung, C.; Nikolai, L.; Lewis, M.; Coutouly, M.A.; Forsythe, I.; Tang, P.; Shrivastava, S.; Jeroncic, K.; Stothard, P.; Amegbey, G.; Block, D.; Hau, D.D.; Wagner, J.; Miniaci, J.; Clements, M.; Gebremedhin, M.; Guo, N.; Zhang, Y.; Duggan, G.E.; Macinnis, G.D.; Weljie, A.M.; Dowlatabadi, R.; Bamforth, F.; Clive, D.; Greiner, R.; Li, L.; Marrie, T.; Sykes, B.D.; Vogel, H.J.; Querengesser, L. HMDB: the Human Metabolome Database. Nucleic Acids Res., 2007, 35(Database issue), D521-526.
9. Yamaguchi, A.; Iida, K.; Matsui, N.; Tomoda, S.; Yura, K.; Go, M. Het-PDB Navi.: A database for protein-small molecule interactions. J. Biochem., 2004, 135(1), 79-84. (Pubitemid 38405164)
10. Goto, S.; Nishioka, T.; Kanehisa, M. LIGAND: chemical database for enzyme reactions. Bioinformatics, 1998, 14(7), 591-599. (Pubitemid 28461580)
11. Kanehisa, M.; Goto, S.; Hattori, M.; Aoki-Kinoshita, K.F.; Itoh, M.; Kawashima, S.; Katayama, T.; Araki, M.; Hirakawa, M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res., 2006, 34(Database issue), D354-357.
12. Creighton, T.E. Proteins: Structures and Molecular Properties. New York: W. H. Freeman & Co.; 1993.
13. Mucchielli-Giorgi, M.H.; Hazout, S.; Tuffery, P. PredAcc: prediction of solvent accessibility. Bioinformatics, 1999, 15(2), 176-177. (Pubitemid 29134734)
14. Tusnady, G.E.; Simon, I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol., 1998, 283(2), 489-506. (Pubitemid 28470424)
15. Peng, H.; Long, F.; Ding, C. Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2005, 27(8), 1226-1238. (Pubitemid 41245053)
16. Niu, B.; Jin, Y.; Lu, L.; Fen, K.; Gu, L.; He, Z.; Lu, W.; Li, Y.; Cai, Y. Prediction of interaction between small molecule and enzyme using AdaBoost. Mol. Divers., 2009.
17. Dubchak, I.; Muchnik, I.; Mayor, C.; Dralyuk, I.; Kim, S.H. Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification. Proteins, 1999, 35(4), 401-407. (Pubitemid 29264836)
18. Frishman, D.; Argos, P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins, 1997, 27(3), 329-335. (Pubitemid 27149285)
19. Chothia, C.; Finkelstein, A.V. The classification and origins of protein folding patterns. Annu. Rev. Biochem., 1990, 59, 1007-1039.
20. Cai, Y.D.; Chou, K.C. Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition. Biochem. Biophys. Res. Commun., 2003, 305(2), 407-411.
21. Jiang, X.; Wei, R.; Zhang, T.; Gu, Q. Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy. Protein Pept. Lett., 2008, 15(4), 392-396. (Pubitemid 351679342)
22. Cai, Y.; He, J.; Li, X.; Feng, K.; Lu, L.; Kong, X.; Lu, W. Predicting protein subcellular locations with feature selection and analysis. Protein Pept. Lett., 2010, 17(4), 464-472.
23. Ding, Y.S.; Zhang, T.L.; Chou, K.C. Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network. Protein Pept. Lett., 2007, 14(8), 811-815.
24. Kandaswamy, K.K.; Pugalenthi, G.; Moller, S.; Hartmann, E.; Kalies, K.U.; Suganthan, P.N.; Martinetz, T. Prediction of apoptosis protein locations with genetic algorithms and support vector machines through a new mode of pseudo amino Acid composition. Protein Pept. Lett., 2010, 17(12), 1473-1479.
25. Shi, R.; Hu, X. Predicting enzyme subclasses by using support vector machine with composite vectors. Protein Pept. Lett., 2010, 17(5), 599-604.
26. Li, S.; Li, H.; Li, M.; Shyr, Y.; Xie, L.; Li, Y. Improved prediction of lysine acetylation by support vector machines. Protein Pept. Lett., 2009, 16(8), 977-983.
27. Li, F.M.; Li, Q.Z. Predicting protein subcellular location using Chou's pseudo amino acid composition and improved hybrid approach. Protein Pept. Lett., 2008, 15(6), 612-616.
28. Liu, T.; Zheng, X.; Wang, C.; Wang, J. Prediction of subcellular location of apoptosis proteins using pseudo amino acid composition: an approach from auto covariance transformation. Protein Pept. Lett., 2010, 17(10), 1263-1269.
29. Ding, H.; Liu, L.; Guo, F.B.; Huang, J.; Lin, H. Identify Golgi Protein Types with Modified Mahalanobis discriminant Algorithm and Pseudo Amino Acid Composition. Protein Pept. Lett., 2010.
30. Grisenti, P.; Magni, A.; Olgiati, V.; Manzocchi, A.; Ferraboschi, P.; Villani, V.; Pucciariello, R.; Celotti, F. Substrate interaction with 5alpha-reductase enzyme: influence of the 17beta-chain chirality in the mechanism of action of 4-azasteroid inhibitors. Steroids, 2001, 66(11), 803-810. (Pubitemid 32884306)
31. von Bulow, R.; Schmidt, B.; Dierks, T.; von Figura, K.; Uson, I. Crystal structure of an enzyme-substrate complex provides insight into the interaction between human arylsulfatase A and its substrates during catalysis. J. Mol. Biol., 2001, 305(2), 269-277. (Pubitemid 32099460)
32. Yudushkin, I.A.; Schleifenbaum, A.; Kinkhabwala, A.; Neel, B.G.; Schultz, C.; Bastiaens, P.I. Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B. Science, 2007, 315(5808), 115-119. (Pubitemid 46196993)
33. Sadasivan, C.; Yee, V.C. Interaction of the factor XIII activation peptide with alpha-thrombin. Crystal structure of its enzyme-substrate analog complex. J. Biol. Chem., 2000, 275(47), 36942-36948. (Pubitemid 32002108)
34. Ondrechen, M.J.; Briggs, J.M.; McCammon, J.A. A model for enzyme-substrate interaction in alanine racemase. J. Am. Chem. Soc., 2001, 123(12), 2830-2834. (Pubitemid 32910708)
35. Cai, Y.D.; Qian, Z.; Lu, L.; Feng, K.Y.; Meng, X.; Niu, B.; Zhao, G.D.; Lu, W.C. Prediction of compounds' biological function (metabolic pathways) based on functional group composition. Mol. Divers., 2008, 12(2), 131-137.