Predicting Metabolic Pathways of Small Molecules and Enzymes Based on Interaction Information of Chemicals and Proteins

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Gao, Yu Fei ^a   Chen, Lei ^b   Cai, Yu Dong ^c   Feng, Kai Yan ^d   Huang, Tao ^e,f,g   Jiang, Yang ^a  

^a CHINA JAPAN UNION HOSPITAL OF JILIN UNIVERSITY   (China)

^b SHANGHAI MARITIME UNIVERSITY   (China)

^c SHANGHAI UNIVERSITY   (China)

^d BGI SHENZHEN   (China)

^e Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^f SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^g MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; PEPTIDES AND PROTEINS; SMALL MOLECULE; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; BIOCHEMISTRY; CHEMICAL INTERACTION; JACKKNIFE TEST; METABOLISM; NONHUMAN; PREDICTION; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; YEAST;

ALGORITHMS; DATABASES, FACTUAL; METABOLIC NETWORKS AND PATHWAYS; METABOLOMICS; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84866640436     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045944     Document Type: Article

References (33)

1. Lu J, Niu B, Liu L, Lu WC, Cai YD, (2009) Prediction of Small Molecules Metabolic Pathways Based on Functional Group Composition. Protein and Peptide Letters 16: 969-976.
2. Kanehisa M, Goto S, (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28: 27-30.
3. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita K, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Research 34: D354-D357.
4. Bairoch A, (1994) The ENZYME data bank. Nucleic Acids Research 22: 3626-3627.
5. Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P, (2008) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 36: D684-688.
6. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic acids research 37: D412-416.
7. Cai YD, Qian Z, Lu L, Feng KY, Meng X, et al. (2008) Prediction of compounds' biological function (metabolic pathways) based on functional group composition. Molecular Diversity 12: 131-137.
8. Hu LL, Chen C, Huang T, Cai YD, Chou KC, (2011) Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions. PLoS ONE 6: e29491.
9. Sharan R, Ulitsky I, Shamir R, (2007) Network-based prediction of protein function. Molecular systems biology 3: 88.
10. Huang T, Shi XH, Wang P, He Z, Feng KY, et al. (2010) Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS ONE 5: e10972.
11. Hu LL, Huang T, Shi X, Lu WC, Cai YD, et al. (2011) Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties. PLoS ONE 6: e14556.
12. Chen L, Zeng WM, Cai YD, Feng KY, Chou KC, (2012) Predicting Anatomical Therapeutic Chemical (ATC) Classification of Drugs by Integrating Chemical-Chemical Interactions and Similarities. PLoS ONE 7: e35254.
13. Bogdanov P, Singh AK, (2010) Molecular Function Prediction Using Neighborhood Features. Ieee-Acm Transactions on Computational Biology and Bioinformatics 7: 208-217.
14. Kourmpetis YAI, van Dijk ADJ, Bink MCAM, van Ham RCHJ, ter Braak CJF, (2010) Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data. PLoS ONE 5: e9293.
15. Hu LL, Huang T, Cai YD, Chou KC, (2011) Prediction of Body Fluids where Proteins are Secreted into Based on Protein Interaction Network. PLoS ONE 6: e22989.
16. Chou KC, Cai YD, (2005) Predicting protein localization in budding yeast. Bioinformatics 21: 944.
17. Chou K, Shen H, (2010) A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0. PLoS ONE 5: e9931.
18. Ng KL, Ciou JS, Huang CH, (2010) Prediction of protein functions based on function-function correlation relations. Computers in Biology and Medicine 40: 300-305.
19. Chou KC, Zhang CT, (1995) Prediction of protein structural classes. Critical reviews in biochemistry and molecular biology 30: 275-349.
20. Chou KC, Shen HB, (2007) Recent progress in protein subcellular location prediction. Analytical Biochemistry 370: 1-16.
21. Chou KC, (2011) Some remarks on protein attribute prediction and pseudo amino acid composition. Journal of theoretical biology 273: 236-247.
22. Chou KC, Shen HB, (2010) Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms. Natural Science 2: 1090-1103.
23. Shao X, Tian Y, Wu L, Wang Y, Jing L, et al. (2009) Predicting DNA-and RNA-binding proteins from sequences with kernel methods. Journal of Theoretical Biology 258: 289-293.
24. Zeng Y, Guo Y, Xiao R, Yang L, Yu L, et al. (2009) Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. Journal of Theoretical Biology 259: 366-372.
25. Li FM, Li QZ, (2008) Predicting Protein Subcellular Location Using Chou's Pseudo Amino Acid Composition and Improved Hybrid Approach. Protein and Peptide Letters 15: 612-615.
26. Lin H, Wang H, Ding H, Chen YL, Li QZ, (2009) Prediction of Subcellular Localization of Apoptosis Protein Using Chou's Pseudo Amino Acid Composition. Acta Biotheoretica 57: 321-330.
27. Chen L, He ZS, Huang T, Cai YD, (2010) Using compound similarity and functional domain composition for prediction of drug-target interaction networks. Medicinal Chemistry 6: 388-395.
28. Sun XD, Huang RB, (2006) Prediction of protein structural classes using support vector machines. Amino Acids 30: 469-475.
29. Huang Y, Li YD, (2004) Prediction of protein subcellular locations using fuzzy k-NN method. Bioinformatics 20: 21-28.
30. Matsuda S, Vert JP, Saigo H, Ueda N, Toh H, et al. (2005) A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Science 14: 2804-2813.
31. Mondal S, Bhavna R, Mohan Babu R, Ramakumar S, (2006) Pseudo amino acid composition and multi-class support vector machines approach for conotoxin superfamily classification. Journal of theoretical biology 243: 252-260.
32. Von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, et al. (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic acids research 33: D433-D437.
33. Kuhn M, Szklarczyk D, Franceschini A, Campillos M, Von Mering C, et al. (2010) STITCH 2: an interaction network database for small molecules and proteins. Nucleic acids research 38: D552-D556.