Applications

Bimal: Bipartite Matching Alignment for the Contact Map Overlap Problem
Citation key	Jain2009
Author	Jain, B. and Obermayer, K.
Title of Book	2009 International Joint Conference on Neural Networks
Pages	1394 – 1400
Year	2009
ISBN	978-1-4244-3553-1, 978-1-4244-3548-7
ISSN	2161-4393
DOI	10.1109/IJCNN.2009.5178901
Publisher	IEEE
Abstract	Email Print Request Permissions Bimal, a fast method for approximately solving the maximum contact map overlap (maxCMO) problem is introduced. The method is based on an approximate model of the maxCMO-problem using the generic bipartite graph matching framework, which is then optimally solved by double dynamic programming. The performance of Bimal has been evaluated in an empirical comparative study including clustering of protein structures according to the SCOP fold's level. Solving about 800 pairwise alignments of medium-sized proteins takes less than 1 min on a 1.7 GHz machine and yields good results for similar protein structures. Bimal accurately classified proteins in agreement with the SCOP classification. In particular, for similar proteins, Bimal provides a good tradeoff between computation speed and solution quality and is because of its high speed useful for solving large-scaled maxCMO applications.