Bioinformatic in Purdue

from [Kihara Bioinformatics Laboratory News]

• 3D-Surfer, a server for rapid protein 3D structure search is released. For a user-uploaded, or selected PDB file, the server searches protein 3D structures with a similar surface shape in the entire PDB database in less than a minute. The conventional RMSD can be also computed to retrieved structures. Characteristic local surfaces, i.e. pockets and protrusions, are identified by our VisGrid algorithm.
• "Combining gene sequence similarity and textual information for gene function annotation" by Luo Si, D. Yu, D. Kihara, & F. Yi, accepted for Information Retrieval.

3D-SURFER is web-based software for protein surface comparison and analysis. The server integrates various repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. It takes less than a second to perform an exhaustive comparison between a single protein surface to all protein structures in the current PDB (80,394 single chain structures of 34,088 total PDB entries). Conveniently, the web interface also renders animated protein rotations, displays CATH codes [Orengo CA, Structure, 1997], and structure alignment calculations using the Combinatorial Extension (CE) algorithm [Shindyalov IN and Bourne PE, Protein Eng, 1998]