Research Interests

Our research interest is in the area of bioinformatics. In the last decade, a large amount of biological data, such as genome/protein sequences, protein 3D structures, and pathway data have become available. These data now enable us to employ comprehensive analysis of relationship between protein sequence, structure and function, evolution of protein families, pathways, and organisms. Especially we are focusing on developing computational methods to predict and analyze protein structure/function, pathway structure, and their applications in genome-scale, or pathway/network scale.

Research Highlights

PFP is our sequence similarity-based protein function prediction server designed to predict GO annotations for a query protein sequence beyond what can be found by searching conventional databases. Visit the server to submit a sequence or read the paper on Protein Science. PFP has achieved the highest total score among participating servers in a function prediciton contest held at AFP-SIG'05, ISMB 2005, and also was the best method in the head-to-head perfomance comparison in the function prediciton category at CASP7.

3D-Surfer is web-based software for protein surface comparison and analysis. The server integrates repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. The surface representation enables a very fast structure search; It takes a couple of seconds to perform an exhaustive comparison between a single protein surface to all protein structures in the current PDB (over 80,000 chains). Visit the server or read the paper on Proteins.