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...
More information can be found on our research projects page here.
|3D-SURFER 2.0 is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. It can compare the protein surface of a single chain, domain, or complex against databases of protein chains, domains, complexes, or a combination of all three, in the latest PDB. Two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accepts a batch job for a large number of database searches. The databases are weekly updated in an automatic way. Visit the server or read the paper on Proteins.|
|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.|
|Sub-AQUA predicts quality of protein 3D structure models by combining a score for assessing the target-template alignment stability and the residue environment. The RMSD value or GDT-TS score of the model to the native structure will be predicted. Check the paper!|
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Kihara Bioinformatics Laboratory is always looking for new people to join the lab. Our current list of openings is available here.