Methods for Linking Protein Structure and Function in Databases

University Of California-San Francisco, San Francisco CA

Investigators

Abstract

The University of California at San Francisco has been awarded a grant to develop new database designs and informatics tools for the discovery, exploration, and application of the links between protein structure and function. Specifically, the project will generate a flexible and rapidly searchable method of representing enzyme function. This representation will include specific protein structural information related to the reaction catalyzed by the enzyme. Methods allowing such reactions to be chained together into novel pathways will also be developed. Enzyme active-site representations which link the structure of a given protein to its specific chemical functionality will be developed as well. This work will be done in concordance with the development of the Structure-Function Linkage Database (SFLD), a resource based upon well-established work on enzyme structure-function relationships in the context of enzyme superfamilies. The successful completion of this project will provide informatics and database tools not currently available in any biological database system, as well as the integration of these methods with other biological database efforts. These new methods will be freely distributed to enable researchers to store, search, and manipulate chemical reactions of biological interest, as well as identify the likely function of new proteins. Workshops to assist researchers and others in using these new resources will be held.