Prediction of Carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Tsai, Keng Chang ^a,f   Jian, Jhih Wei ^a,b,c   Yang, Ei Wen ^a,b   Hsu, Po Chiang ^a   Peng, Hung Pin ^a,b,c   Chen, Ching Tai ^a,b,d   Chen, Jun Bo ^a,e   Chang, Jeng Yih ^a   Hsu, Wen Lian ^b   Yang, An Suei ^a  

^a GENOMICS RESEARCH CENTER   (Taiwan)

^b INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^c NATIONAL YANG MING UNIVERSITY   (Taiwan)

^d NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^e NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^f NATIONAL RESEARCH INSTITUTE OF CHINESE MEDICINE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; CARBOHYDRATE ANTIBODY; CARBOHYDRATE LIGAND; LIGAND; UNCLASSIFIED DRUG;

ACCURACY; AMINO ACID COMPOSITION; ANALYTIC METHOD; ANALYTICAL PARAMETERS; ANTIBODY COMBINING SITE; ARTICLE; ATOM; BINDING SITE; BINDING SITE GEOMETRY; CROSS VALIDATION; HYDROGEN BOND; LEARNING ALGORITHM; NON COVALENT CARBOHYDRATE BINDING SITE; NONBIOLOGICAL MODEL; PREDICTION; PROTEIN CARBOHYDRATE INTERACTION; PROTEIN STRUCTURE; QUALITY CONTROL; SENSITIVITY ANALYSIS; SURFACE PROPERTY; THREE DIMENSIONAL PROBABILITY DENSITY MAP; VALIDATION PROCESS;

ARTIFICIAL INTELLIGENCE; BINDING SITES; CARBOHYDRATES; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84864371562     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040846     Document Type: Article

References (23)

1. Lebrilla CB, An HJ, (2009) The prospects of glycan biomarkers for the diagnosis of diseases. Mol Biosyst 5: 17-20.
2. Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, et al. (2009) Essentials of Glycobiology. 2nd edition Cold Spring Harbor (NY) Cold Spring Harbor Laboratory Press; chapter 20: Eubacteria and Archaea.
3. Weis WI, Drickamer K, (1996) Structural basis of lectin-carbohydrate recognition. Annu Rev Biochem 65: 441-473.
4. Toone EJ, (1994) Structure and energetics of protein-carbohydrate complexes. Current Opinion in Structural Biology 4: 719-728.
5. Vyas NK, (1991) Atomic features of protein-carbohydrate interactions. Current Opinion in Structural Biology 1: 732-740.
6. Quiocho FA, (1986) Carbohydrate-binding proteins: tertiary structures and protein-sugar interactions. Annu Rev Biochem 55: 287-315.
7. Quiocho FA, (1989) Protein-Carbohydrate Interactions: Basic Molecular Features. Pure Appl Chem 61: 1293-1306.
8. Taroni C, Jones S, Thornton JM, (2000) Analysis and prediction of carbohydrate binding sites. Protein Eng 13: 89-98.
9. Shionyu-Mitsuyama C, Shirai T, Ishida H, Yamane T, (2003) An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins. Protein Eng 16: 467-478.
10. Malik A, Ahmad S, (2007) Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network. BMC Struct Biol 7: 1.
11. Kulharia M, Bridgett SJ, Goody RS, Jackson RM, (2009) InCa-SiteFinder: a method for structure-based prediction of inositol and carbohydrate binding sites on proteins. J Mol Graph Model 28: 297-303.
12. Nassif H, Al-Ali H, Khuri S, Keirouz W, (2009) Prediction of protein-glucose binding sites using support vector machines. Proteins 77: 121-132.
13. Chen CT, Yang EW, Hsu HJ, Sun YK, Hsu WL, et al. (2008) Protease substrate site predictors derived from machine learning on multilevel substrate phage display data. Bioinformatics 24: 2691-2697.
14. Yu CM, Peng HP, Chen IC, Lee YC, Chen JB, et al. (2012) Rationalization and design of the complementarity determining region sequences in an antibodyantigen recognition interface. PLoS One 7: e33340.
15. McConkey BJ, Sobolev V, Edelman M, (2003) Discrimination of native protein structures using atom-atom contact scoring. Proceedings of the National Academy of Sciences of the United States of America 100: 3215-3220.
16. Rumelhart DE, Hinton GE, Williams RJ, (1986) Learning internal representations by error propagation MIT Press pp. 318-362.
17. Burges CJC, (1998) A tutorial on support vector machines for pattern recognition. Data Min Knowl Discov 2: 121-167.
18. Chang C-C, Lin C-J, (2001) LIBSVM: A library for support vector machines.
19. Breiman L, (1996) Bagging predictors. Mach Learn 24: 123-140.
20. Manning CD, Raghavan P, Schutze H, (2007) An introduction to information retrieval Cambridge, England Cambridge University Press.
21. Reidmiller M, Braun H, (1993) A direct adaptive method for faster backpropagation learning: the RPROP algorithm. in IEEE Int. pp. 586-591 Conf Neural Networks.
22. Riedmiller M, (1994) Rprop-Description and Implementation Details Technical Report University of Karlsruhe.
23. Laskowski RA, Thornton JM, Humblet C, Singh J, (1996) X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J Mol Biol 259: 175-201.