Research Projects

For more detailed information, please refer to related papers published by our group (a number in a parenthesis speficies a reference in the publication page) and also our software.

Protein Structure Prediction

Protein tertiary structure provides indispensable information for elucidating protein function and evolution. We are developing computational methods for predicting protein tertiarty structure from sequence [35, 23, 19] and methods for error estimation of computational models [31]. We have developed a database of predicted structure models of E. coli, EcoliPredict, which is a part of EcoliHub Project.

Protein Surface Analysis

Protein surface is where function of a protein realizes. Especially interaction with proteins and chemical compounds occur at a specific site of a protein surface. Hence, finding characteristics sites for protein function, e.g. active sites of enzymes, protein interaction interface, is a promising way to predict function of a protein. The aims of this project include development of methods for protein surface shape comparison for fast database search [34] and characterization of surface geometrical property of proteins [30, 28]. We have developed 3D-Surfer , web-based software for fast protein comparison and surface analysis.

Protein Function Prediction

Function annotation of genes is a foundation of almost any molecular biology studies. Conventional methods for function annotation are homology search methods, such as BLAST and FASTA. These methods perform well when obvious homologs exist for a query protein, but don't provide any functional information otherwise. As a consequence, typically about only half of genes are annotated in a newly sequences genome. For a large scale omics analysis, it is helpful if function annotation coverage is larger even with less specific or low-resolution function [32, 26]. The goal of this project is to develop methods which can predict function to a larger number of genes than conventional homology search by providing low-resolution function when necessary witout losing accuracy. Our method, PFP [22], won the best prediction method in CASP7 and Automatic Function Prediction Meeting (AFP-SIG, ISMB 2005). Please try our PFP website .

Sequence Analysis of Intergenic Regions of Genomes

Intergenic regions contain important information for gene regulation. In recent years various families of small non-coding RNAs (sRNAs) have been discovered both in bacterial and eukaryotic genomes. We have developed an ensemble approach of DNA motif discovery, which outperforms standalone programs [24, 20]. We have also computationally identified sRNAs in 30 bacterial genomes and conducted comparative study [27].