Maximum cliques in protein structure comparison

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6049 LNCS, Issue , 2010, Pages 106-117

  Malod Dognin, Noël ^a   Andonov, Rumen ^b   Yanev, Nicola ^c,d  

^a SOUTH WEST UNIVERSITY NEOFIT RILSKI   (Bulgaria)

^b UNIVERSITÉ DE RENNES 1   (France)

^c UNIVERSITY OF SOFIA   (Bulgaria)

^d BULGARIAN ACADEMY OF SCIENCES   (Bulgaria)

Author keywords

Branch and bound; Combinatorial optimization; K partite graphs; Maximum clique problem; Protein structure comparison

Indexed keywords

AUTOMATIC CLASSIFICATION; BRANCH AND BOUNDS; K-PARTITE GRAPH; MAIN CHARACTERISTICS; MAXIMUM CLIQUE; MAXIMUM CLIQUE PROBLEMS; PROTEIN STRUCTURE COMPARISON; PROTEIN STRUCTURES;

ALGORITHMS; ALIGNMENT; COMBINATORIAL OPTIMIZATION; GRAPHIC METHODS; LINEAR PROGRAMMING; MOLECULAR BIOLOGY; PROBLEM SOLVING;

PROTEINS;

EID: 78650670093     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-13193-6_10     Document Type: Conference Paper

References (17)

1. Godzik, A.: The structural alignment between two proteins: Is there a unique answer? Protein Science (7), 1325-1338 (1996).
2. Sierk, M., Kleywegt, G.: Déjà vu all over again: Finding and analyzing protein structure similarities. Structure 12(12), 2103-2111 (2004).
3. Konc, J., Janezic, D.: An efficient branch-and-bound algorithm for finding a maximum clique. Discrete Mathematics and Theoretical Computer Science 58, 220 (2003).
4. Tomita, E., Seki, T.: An improved branch and bound algorithm for the maximum clique problem. Communications in Mathematical and in Computer Chemistry/MATCH 58, 569-590 (2007).
5. Östergård, P.R.J.: A fast algorithm for the maximum clique problem. Discrete Applied Mathematics 120(1-3), 197-207 (2002).
6. Andreeva, A., Howorth, D., Chandonia, J.M., Brenner, S., Hubbard, T., Chothia, C., Murzin, A.: Data growth and its impact on the SCOP database: new developments. Nucl. Acids Res. 36, 419-425 (2007).
7. Strickland, D., Barnes, E., Sokol, J.: Optimal protein structure alignment using maximum cliques. Oper. Res. 53(3), 389-402 (2005).
8. Karp, R.: Reducibility among combinatorial problems. Complexity of Computer Computations 6, 85-103 (1972).
9. Bomze, I., Budinich, M., Pardalos, P., Pelillo, M.: The maximum clique problem. Handbook of Combinatorial Optimization (1999).
10. Gibrat, J.F., Madej, T., Bryant, S.: Surprising similarities in structure comparison. Current Opinion in Structural Biology 6, 377-385 (1996).
11. Godzik, A., Skolnick, J.: Flexible algorithm for direct multiple alignment of protein structures and sequences. CABIOS 10, 587-596 (1994).
12. Andonov, R., Yanev, N., Malod-Dognin, N.: An efficient lagrangian relaxation for the contact map overlap problem. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 162-173. Springer, Heidelberg (2008).
13. Caprara, A., Carr, R., Israil, S., Lancia, G., Walenz, B.: 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. J. Comput. Biol. 11(1), 27-52 (2004).
14. Fredman, M.: On computing the length of longest increasing subsequences. Discrete Mathematics 11, 29-35 (1975).
15. Martin, J., Letellier, G., Marin, A., Taly, J.F., de Brevern, A., Gibrat, J.F.: Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Structural Biology 5, 17 (2005).
16. Lancia, G., Carr, R., Walenz, B., Istrail, S.: 101 optimal pdb structure alignments: a branchand- cut algorithm for the maximum contact map overlap problem. In: RECOMB 2001: Proceedings of the fifth annual international conference on Computational biology, pp. 193-202 (2001).
17. Lerman, I.: Likelihood linkage analysis (lla) classification method (around an example treated by hand). Biochimie 75(5), 379-397 (1993).