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  Joining softassign and dynamic programming for the contact map overlap problem

Brijnesh, J. J., & Lappe, M. (2007). Joining softassign and dynamic programming for the contact map overlap problem. Berlin; Heidelberg: Springer Berlin / Heidelberg.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-82EB-D Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-82EC-B
Genre: Proceedings

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 Creators:
Brijnesh, J. Jain, Author
Lappe, Michael1, Author              
Affiliations:
1Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433554              

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 Abstract: Comparison of 3-dimensional protein folds is a core problem in molecular biology. The Contact Map Overlap (CMO) scheme provides one of the most common measures for protein structure similarity. Maximizing CMO is, however, NP-hard. To approximately solve CMO, we combine softassign and dynamic programming. Softassign approximately solves the maximum common subgraph (MCS) problem. Dynamic programming converts the MCS solution to a solution of the CMO problem. We present and discuss experiments using proteins with up to 1500 residues. The results indicate that the proposed method is extremely fast compared to other methods, scales well with increasing problem size, and is useful for comparing similar protein structures.

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Language(s): eng - English
 Dates: 2007
 Publication Status: Published in print
 Pages: 479 pp
 Publishing info: Berlin; Heidelberg : Springer Berlin / Heidelberg
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 337063
ISBN: 978-3-540-71232-9
ISSN: 0302-9743
DOI: 10.1007/978-3-540-71233-6_32
URI: http://springerlink.com/content/akl718172228471l/fulltext.pdf
 Degree: -

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Title: First International Conference, BIRD 2007
Place of Event: Berlin
Start-/End Date: 2007-03-12 - 2007-03-14

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Title: Lecture Notes in Computer Science
Source Genre: Series
 Creator(s):
Hochreiter Wagner R., S., Editor
Affiliations:
-
Publ. Info: -
Pages: - Volume / Issue: 4414 Sequence Number: - Start / End Page: - Identifier: -