title: Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains.
abstract: 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.
authors.affiliation: Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA.
authors.forename: Ashwani
authors.initials: A
authors.lastname: Jha
authors.affiliation: Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA.
authors.forename: K M
authors.initials: KM
authors.lastname: Flurchick
authors.affiliation: Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA.
authors.forename: Marwan
authors.initials: M
authors.lastname: Bikdash
authors.affiliation: Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA.
authors.forename: Dukka B
authors.identifier: 0000-0001-5590-5403
authors.initials: DB
authors.lastname: Kc
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics; D019295:Computational Biology; D011487:Protein Conformation; D000072417:Protein Domains / Q000235:genetics*; D011506:Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D011506:Proteins