A finding maximal clique algorithm for predicting loop of protein structure

In this paper we equate the problem of predicting the loop 3D structure in the comparative modeling to a problem of finding the maximal clique with the best weight. Each possible conformation of a residue in a loop sequence is represented as a node in a graph. Edges are then drawn between pairs of nodes that are consistent with each other. Edge and nodes are weighted according to some fixed criteria. Once the entire graph is constructed, all the maximal sets of cliques are found using an algorithm of artificial neural network models. The cliques with the best weights represent the optimal conformation of the region of loop sequence.

[1]  S. Vishveshwara,et al.  Identification of side-chain clusters in protein structures by a graph spectral method. , 1999, Journal of molecular biology.

[2]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[3]  R Samudrala,et al.  A graph-theoretic algorithm for comparative modeling of protein structure. , 1998, Journal of molecular biology.

[4]  A. Sali,et al.  Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Saraswathi Vishveshwara,et al.  Classification of polymer structures by graph theory , 1999 .

[6]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[7]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[8]  F. Collins,et al.  Principles of Biochemistry , 1937, The Indian Medical Gazette.

[9]  H. Zhang,et al.  Conformational analysis of two glycoproteins: a Monte Carlo simulated annealing approach using a soft-sphere potential. , 1996, Carbohydrate research.

[10]  Andrew P. French,et al.  Instant Notes in Bioinformatics , 2002 .

[11]  Hongyi Zhou,et al.  Folding rate prediction using total contact distance. , 2002, Biophysical journal.

[12]  Lavery,et al.  Mathematical Challenges from Theoretical/Computational Chemistry. , 1995 .

[13]  Hongyi Zhou,et al.  The dual role of a loop with low loop contact distance in folding and domain swapping , 2002, Protein science : a publication of the Protein Society.

[14]  C Venclovas,et al.  Criteria for evaluating protein structures derived from comparative modeling , 1997, Proteins.

[15]  K. Fidelis,et al.  Comparison of systematic search and database methods for constructing segments of protein structure. , 1994, Protein engineering.

[16]  J Moult,et al.  An algorithm which predicts the conformation of short lengths of chain in proteins , 1986 .

[17]  P Willett,et al.  Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. , 1993, Journal of molecular biology.

[18]  R. Samudrala,et al.  An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.