Award details

Automated Grid-aware three-tier protocol for protein structure comparison

Principal Investigator / Supervisor Professor Natalio Krasnogor
Co-Investigators /
Dr Helen Ashman, Dr Timothy Brailsford, Professor Edmund Burke, Professor Jonathan Hirst
Institution University of Nottingham
DepartmentSchool of Computer Science
Funding typeResearch
Value (£) 63,614
TypeResearch Grant
Start date 01/04/2005
End date 30/09/2006
Duration18 months


Any advancement in structural similarity measures will impact on a variety of bioinformatics related endeavours. Although there has been an enormous amount of research effort dedicated to the procurement of structural comparison methodologies there is still no general agreement on which is the best similarity measure to use. A variety of structure comparison methods have been used in classification servers such as SCOP [MurBreHubCho95], DALI [HolSan93], LGA [Zem03], CATH [OreMicJonJonSwiTho97], and others. A more recent approach for structural matching is based on the maximum alignment (also called overlap) of proteins contact maps. The optimal alignment of contact maps (i.e. The Maximum Contact Map Overlap) is the only structural matching method for which exact upper and lower bounds can be computed and compared [CapLan02]. Additionally, in [KraPel04], we proposed the universal similarity metric as a means to capture every other similarity metric for protein structures. In that paper we suggested a two-tier protocol for protein structure comparison and similarity assessment that exploited the strength of both the Universal Similarity Metric and the Maximum Contact Map Overlap measure. Although this two-tier protocol is well understood from a mathematical and computational point of view it has not been tested in the field by biologists. We propose to use grid technology and novel interfaces to enhance and bring this new similarity and structure comparison method to the biological research community by making it publicly available, easy to use, compare and integrate with other (pre-existing) software. We will undertake the implementation of an extended (three-tier) protocol for protein structure comparison building on our recent research progress. The new software will be grid-aware, publicly accessible and will have both an intuitive visual interface and also a powerful programmatic application interface (API). It will extend the two-tier protocol described in [KraPel04] by integrating the Lagrangian Relaxation and metaheuristic method for Maximum Contact Map Overlaps of [CapLan02,Kra04]. The third layer of the proposed protocol will harvest publicly available protein comparison services and will integrate the results of the initial two layers with those harvested from existing software and databases.


Committee Closed Committee - Biomolecular Sciences (BMS)
Research TopicsX – not assigned to a current Research Topic
Research PriorityX – Research Priority information not available
Research Initiative EDF (e-science Development Fund) (EDF) [2003-2005]
Funding SchemeX – not Funded via a specific Funding Scheme
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