SBIR-STTR Award

Because of the complexity of protein phosphoregulation and the large number of phosphorylation sites, there is a significant need for a bioinformatics resource dedicated to collecting, organizing and analyzing information centered around specific sites of protein phosphorylation (phosphosites). Our long-term goal is to establish a curated database (PhosphoSiteDB) organized around "in vivo" phosphosites in the human and mouse. It will be populated with information from literature reports and our own in-house discovery program. Information will center around phosphosites, including information about (1) "in vivo" sites of phosphorylation, including their association with domains and known motifs, (2) names of kinases/phosphatases that directly regulate the phosphorylation state of a given phosphosite, (3) names of proteins that interact with the phosphosite, (4) and a limited number of observations that result from those state changes including disease associations and diagnostic relevance. The goals of this Phase I application are (1) to design the specifications for the database structure consistent with our long term goals, and (2) to expand and organize our in-house information on important regulatory phosphosites into a simple functional database that will eventually be transferred in PhosphoSiteDB. Phase II will see the actual coding, beta testing, and deployment of (V1.0) PhosphoSiteDB. In the initial release, the content will be limited to information curated from "in vivo" human and mouse primary literature reference data.

Thesaurus Terms:
computer system design /evaluation, molecular biology information system, molecular site, phosphorylation informatics, phosphoprotein phosphatase, protein kinase biotechnology

Protein phosphorylation is a ubiquitous mechanism that helps regulate most cellular processes including growth, differentiation, plasticity, and memory. Additionally, alterations in the regulation of phosphorylation are implicated in the etiology of many human diseases. The goal of the application is to build the Phosphosite Database (PSDB), a curated database dedicated to aggregating important information about in vivo protein phosphorylation sites (phosphosites) in human and mouse proteins. It will provide the user with curated information about phosphosites, including sequence, structure and regulatory mechanisms. This application describes the methods that will be used to develop and deploy the database, the strategy for rapidly populating it with information useful to the bench researcher as well as the bioinformatician, and lastly proposes to develop software that supports sequence mining and modeling of phosphorylation cascades. Commercialization Plans. The commercialization plan for PSDB includes: 1) public access to all data published prior to a six month period. Since there is no other systematic resource of this type, the information in PSDB should be of significant value to many scientists in the field; 2) limited access to up-to-date public information about particular phosphosites will be available to customers of CST antibodies and other products; 3) full access to up-to-date public information about all PSDB phosphosites will be available to standard subscribers to the PSDB; and 4) full access to up-to-date public information and proprietary information contained in PSDB will be available to premier subscribers to the PSDB