Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains.
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 deter...
| Publicado en: | BioMed Research International Vol. 2016; pp. 1 - 10 |
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| Autores principales: | , , , |
| Formato: | algorithm research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
9/26/2016
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=118346685&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 118346685 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 9/26/2016 vid: 2016 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 118346685 118346685 118346685 10.1155/2016/4628592 118346685 ppf: 1 ppct: 9 formats: fmt: @attributes: type: P tig: atl: Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains. aug: au: Jha, Ashwani Flurchick, K. M. Bikdash, Marwan KC, Dukka B. affil: Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA sug: subj: Proteins Analysis Algorithms Evaluation Molecular Structure Evaluation Bioinformatics Time Factors Random Sample Funding Source ab: 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. pubtype: Academic Journal doctype: algorithm research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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