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Investigators at University of London Imperial College Report Findings in Proteomics

June 24, 2014



By a News Reporter-Staff News Editor at Information Technology Newsweekly -- Research findings on Proteomics are discussed in a new report. According to news originating from London, United Kingdom, by VerticalNews correspondents, research stated, "Protein structure alignment is key for transferring information from well-studied proteins to less studied ones. Structural alignment identifies the most precise mapping of equivalent residues, as structures are more conserved during evolution than sequences."

Our news journalists obtained a quote from the research from the University of London Imperial College, "Among the methods for aligning protein structures, maximum Contact Map Overlap (CMO) has received sustained attention during the past decade. Yet, known algorithms exhibit modest performance and are not applicable for large-scale comparison. Graphlets are small induced subgraphs that are used to design sensitive topological similarity measures between nodes and networks. By generalizing graphlets to ordered graphs, we introduce GR-Align, a CMO heuristic that is suited for database searches. On the Proteus_300 set (44 850 protein domain pairs), GR-Align is several orders of magnitude faster than the state-of-the-art CMO solvers Apurva, MSVNS and AlEigen7, and its similarity score is in better agreement with the structural classification of proteins. On a largescale experiment on the Gold-standard benchmark dataset (3 207 270 protein domain pairs), GR-Align is several orders of magnitude faster than the state-of-the-art protein structure comparison tools TM-Align, DaliLite, MATT and Yakusa, while achieving similar classification performances. Finally, we illustrate the difference between GR-Align's flexible alignments and the traditional ones by querying a flexible protein in the Astral-40 database (11 154 protein domains)."

According to the news editors, the research concluded: "In this experiment, GR-Align's top scoring alignments are not only in better agreement with structural classification of proteins, but also that they allow transferring more information across proteins."

For more information on this research see: GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity. Bioinformatics, 2014;30(9):1259-1265. Bioinformatics can be contacted at: Oxford Univ Press, Great Clarendon St, Oxford OX2 6DP, England. (Oxford University Press - www.oup.com/; Bioinformatics - bioinformatics.oxfordjournals.org)

The news correspondents report that additional information may be obtained from N. Malod-Dognin, University of London Imperial College, Dept. of Comp, London SW7 2AZ, United Kingdom.

Keywords for this news article include: London, Europe, Proteomics, United Kingdom, Protein Structure

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Source: Information Technology Newsweekly


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