Development and Dissemination of e-Protein: A distributed pipeline for annotation using GRID technology

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E-protein (www.e-protein.org) is a BEP-1 GRID pilot project entitled `A distributed pipeline for structure-based proteome annotation using GRID technology¿. The project involves three groups ¿ Imperial College London (Professors Sternberg and Darlington), UCL (Professor Jones and Dr Sorensen) and the EBI (Professor Thornton and Dr Birney). The aim of e-protein is to provide a structure-based annotation of the proteins in the major genomes linking resources at the three sites by GRID technology. We are on track to deliver the project with highlights of the work to date being: - The development and analysis of databases of proteome annotation at Imperial (3D-Genomics) and UCL (GTD and Gene3D). ¿ The development of databases providing functional annotation of proteins using structural information (EBI). ¿ The development of protein DAS that provides a single web-based portal to access the different proteome annotation databases. ¿ The demonstration of inter-site distributed computing for proteome annotation using the Jyde software protocol developed at UCL. ¿ The development of the ICENI protocol (at Imperial) for capture the workflow of the proteome annotation pipeline and map it to multiple Grid resources, providing the capability of true resource brokering. The project is funded by the BBSRC/DTI, runs for 39 months and employs 6 PDRAs. At each site we have one protein bioinformatician and one computer scientist. The first posts started in May 2002 and will end early September 2005 whilst other posts started later. This proposal is for support for three postdoctoral workers each for 4 months that will ensure the full team is working together for four months post September. This funding will enable us to undertake the following topics in the further development and the dissemination of the e-protein project. ¿ The incorporation of three-dimensional structural models into 3D-Genomics structural annotation database at Imperial. ¿ The extension to all protein sequences of the functional annotation of possible ligand binding regions based on data from crystallised protein structures at the EBI. ¿ The dissemination to the community of the Jyde software for distributed use of computing resources. ¿ The incorporation into ICENI of features related to remote database accessibility and use of OGSA-DAI (Open Grid Services Architecture, Data Access and Integration). ¿ The dissemination of protein DAS into BioSapiens ¿ the EU network of Excellence for Genome annotation (http:www.BioSapiens.info)