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Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains
Joint Authors
KC, Dukka B.
Jha, Ashwani
Flurchick, K. M.
Bikdash, Marwan
Source
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-09-26
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
Internally symmetric proteins are proteins that have a symmetrical structure in their monomeric single-chain form.
Around 10–15% of the protein domains can be regarded as having some sort of internal symmetry.
In this regard, we previously published SymD (symmetry detection), an algorithm that determines whether a given protein structure has internal symmetry by attempting to align the protein to its own copy after the copy is circularly permuted by all possible numbers of residues.
SymD has proven to be a useful algorithm to detect symmetry.
In this paper, we present a new parallelized algorithm called Parallel-SymD for detecting symmetry of proteins on clusters of computers.
The achieved speedup of the new Parallel-SymD algorithm scales well with the number of computing processors.
Scaling is better for proteins with a larger number of residues.
For a protein of 509 residues, a speedup of 63 was achieved on a parallel system with 100 processors.
American Psychological Association (APA)
Jha, Ashwani& Flurchick, K. M.& Bikdash, Marwan& KC, Dukka B.. 2016. Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains. BioMed Research International،Vol. 2016, no. 2016, pp.1-9.
https://search.emarefa.net/detail/BIM-1097830
Modern Language Association (MLA)
Jha, Ashwani…[et al.]. Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains. BioMed Research International No. 2016 (2016), pp.1-9.
https://search.emarefa.net/detail/BIM-1097830
American Medical Association (AMA)
Jha, Ashwani& Flurchick, K. M.& Bikdash, Marwan& KC, Dukka B.. Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains. BioMed Research International. 2016. Vol. 2016, no. 2016, pp.1-9.
https://search.emarefa.net/detail/BIM-1097830
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1097830