PROTEIN DATA BANK BIOMEDICAL COMMUNITY SERVICES

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. (A) OBJECTIVES The RCSB Protein Data Bank (PDB) is an international repository for three-dimensional macromolecular structure data (Berman et al., 2000). The RCSB team, directed by Prof. Helen Berman, is in the process of applying for a new five-year grant to operate the PDB. This collaborative project will synergize activities proposed in each respective projects renewal. As a result both projects will be stronger and more valuable to a community of users than would otherwise be the case. This synergistic effort has the following goals for each resource: For PDB: + NBCR will provide a vehicle to distribute and use protein functional site search information generated by the PDB and provided as a Web service. The method of site search is yet to be determined and will be evaluated by the PDB in the early stages of the renewal. The intent is to provide details of similar binding sites that have implications for a variety of studies from evolutionary relationships to drug discovery. + NBCR will provide a distributed environment to support the computation of data associated with 3-dimensional structure comparison. The PDB renewal calls for these data initially being calculated by the FatCat method (Ye and Godzik 2004) that provides for protein flexibility. Later other methods will be evaluated. In either case computation of an all-by-all protein structure comparison is a high performance task that can benefit from the NBCR infrastructure. For NBCR: PDB will provide high visibility and audience for services that include: + Passing the results of structure comparisons and other data to applications through NBCR middleware. + Provision of a testbed for grid services. + Provision by NBCR of electrostatic data to be included as part of PDB services (this provision was not in the PDB renewal application but is deemed a useful addition).