Area of Research

Dr. Daisuke Kihara
Principal Investigator

Our research interests lie in the area of bioinformatics. We employ computational methods to elucidate intertwined relationships between protein/gene sequences, structure, function, interactions, genome, and pathways. The ultimate goal of our research projects is to obtain new, comprehensive understanding of how structures and functions are coded in molecular sequences and how functions of molecules are orchestrated in a cell.

Specifically, we develop and apply novel computational methods for...

• Predicting protein structure from sequence
• Predicting protein function from sequence and structure
• Predicting protein-protein and protein-ligand interactions
• Predicting functional sites in sequences
• Genome-scale function and structure annotation
• Analyzing functional units in networks

More information can be found on our research projects page here.

Research Highlights

	ESG is our new sequence similarity-based protein function prediction server. In essence, it further applies PFP iteratively and obtains superior performance in terms of prediction accuracy. Visit the server to submit a sequence or read the paper in Bioinformatics. ESG annotates query sequences with Gene Ontology terms by assigning probability to each annotation. Statistical framework of ESG improves the prediction accuracy by iteratively taking into account the neighborhood of query protein in the similarity based sequence space.
	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.