A finding maximal clique algorithm for predicting loop of protein structure

Applied Mathematics and Computation

Volumn 180, Issue 2, 2006, Pages 676-682

  Shi, Xiaohong ^a   LuoLiang, ^a   Wan, Yan ^a   Xu, Jin ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Algorithm; Loop; Maximal clique; Neural network; Prediction; Protein structure

Indexed keywords

CONFORMATIONS; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; NEURAL NETWORKS; PROTEINS;

CLIQUE ALGORITHM; LOOP; MAXIMAL CLIQUE; PROTEIN STRUCTURE;

ALGORITHMS;

EID: 33748972279     PISSN: 00963003     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.amc.2006.01.009     Document Type: Article

References (19)

1. Horton H.R., Moran L.A., Ochs R.S., Rawn D.J., and Scrimgeour K.G. Principles of Biochemistry (2002), Science Press and Pearson Education North Asia Limited
2. Dayhoff M.O. Atlas of protein sequence and structure. National Biomedical Research Foundation vol. 5 (1972), Georgetown University, Washington, DC
3. Westhead D.R., Parish J.H., and Twyman R.M. Instant Notes in Bioinformatics (2002), BIOS Scientific Publishers Limited
4. Fiser A., Do G., and Sali A. Modeling of loops in protein structures. Protein Sci. 9 (2000) 1753-1773
5. Venclovas C., Zemla A., Fidelis K., and Moult J. Numerical criteria for evaluating protein structures derived from comparative modeling. Proteins: Struct. Funct. Gent. Sup. 1 (1997) 7-13
6. Sanchez R., and Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. USA 95 (1998) 13597-13602
7. Zhou H., and Zhou Y. Folding rate prediction using total contact distance. Biophysical 82 January (2002) 458-463
8. Zhou Y., Zhou H., and Linhananta A. The dual role of a loop with low loop contact distance in folding and domain swapping. Protein Sci. 11 (2002) 1695-1701
9. National Research Council. Mathematical Challenges from Theoretical/Computational Chemistry (1995), National Academy Press, Washington, DC
10. Grindley H., et al. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229 (1993) 707-721
11. Zhang H.Y., et al. Conformational analysis of two glycoproteins: a Monte Carlo simulated annealing approach using soft-sphere potential. Carbohydr. Res. 284 (1996) 25-34
12. Samudrala R., and Moult J. A graph-theoretic algorithm for comparative modeling of protein structure. J. Mol. Biol. 279 (1998) 287-302
13. Patra S.M., and Vishveshwara S. Classification of polymer structures by a graph theory. Int. J. Quantum Chem. 71 (1998) 349-356
14. Kannan N., and Vishveshwara S. Identification of side-chain clusters in protein structures by a graph spectral method. J. Mol. Biol. 292 (1999) 441-464
15. Samudrala R., and Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol. 275 (1998) 895-916
16. Xu J., and Bao Z. The algorithm for maximal cliques and independent set based on artificial network. Electric Science Application 3 (1993) 46-57
17. M. Braxenthaler, R. Samudrala, J. Pedersen, R. Luo, B. Milash, J. Moult, PROSTAR: The protein potential test site, 1997. Available from: .
18. Moult J., and James M.N. An algorithm which predicts the conformation of short lengths of chain in proteins. J. Mol. Graphics 4 (1986) 180-187
19. Fidelis K., Stern P., Bacon D., and Moult J. Comparison of systemic search and database methods for constructing segments of protein structure. Protein Eng. 7 (1994) 953-960