Structural proteomics: methods in deriving protein structural information and issues in data management

Structural proteomics is an emerging paradigm that is gaining importance in the post-genomic era as a valuable discipline to process the protein target information being deciphered. The field plays a crucial role in assigning function to sequenced proteins, defining pathways in which the targets are involved, and understanding structure-function relationships of the protein targets. A key component of this research sector is accessing the three-dimensional structures of protein targets by both experimental and theoretical methods. This then leads to the question of how to store, retrieve, and manipulate vast amounts of sequence (1-D) and structural (3-D) information in a relational format so that extensive data analysis can be achieved. We at SBI have addressed both of these fundamental requirements of structural proteomics. We have developed an extensive collection of three-dimensional protein structures from sequence data and have implemented a relational architecture for data management. In this article we will discuss our approaches to structural proteomics and the tools that life science researchers can use in their discovery efforts.