Solving Maximum Clique Problem for Protein Structure Similarity

Malod-Dognin, Noël, Andonov, Rumen, and Yanev, Nicola. "Solving Maximum Clique Problem for Protein Structure Similarity." Serdica Journal of Computing 4.1 (2010): 93-100. <http://eudml.org/doc/11378>.

@article{Malod2010,
abstract = {Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK.* This work is supported by the ANR project PROTEUS "ANR-06-CIS6-008", by the Brittany Region and by the Bulgarian NSF project DO 02-359/2008.},
author = {Malod-Dognin, Noël, Andonov, Rumen, Yanev, Nicola},
journal = {Serdica Journal of Computing},
keywords = {Protein Structure Comparison; Maximum Clique; K-Partite Graphs; Integer Programming; Branch and Bound; protein structure comparison; maximum clique; k-partite graphs; integer protgramming; branch and bound},
language = {eng},
number = {1},
pages = {93-100},
publisher = {Institute of Mathematics and Informatics Bulgarian Academy of Sciences},
title = {Solving Maximum Clique Problem for Protein Structure Similarity},
url = {http://eudml.org/doc/11378},
volume = {4},
year = {2010},
}

TY - JOUR
AU - Malod-Dognin, Noël
AU - Andonov, Rumen
AU - Yanev, Nicola
TI - Solving Maximum Clique Problem for Protein Structure Similarity
JO - Serdica Journal of Computing
PY - 2010
PB - Institute of Mathematics and Informatics Bulgarian Academy of Sciences
VL - 4
IS - 1
SP - 93
EP - 100
AB - Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK.* This work is supported by the ANR project PROTEUS "ANR-06-CIS6-008", by the Brittany Region and by the Bulgarian NSF project DO 02-359/2008.
LA - eng
KW - Protein Structure Comparison; Maximum Clique; K-Partite Graphs; Integer Programming; Branch and Bound; protein structure comparison; maximum clique; k-partite graphs; integer protgramming; branch and bound
UR - http://eudml.org/doc/11378
ER -