Maebashi Institute of Technology Protein Informatics Laboratory


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Protein Informatics Laboratory
Maebashi Institute of Technology

The goal of Protein Informatics group is to understand living systems by focusing on protein structures encoded in genome sequences. To achieve this goal, we are using computer technology to dig up knowledge from biological databases. Biological data has been rapidly accumulated after entering this century, and one of the keys in the recent biology is to make good use of such data.

We are particularly focusing on intrinsically disordered proteins (IDPs). IDPs do not adopt unique three-dimensional (3D) structure under physiological conditions. They are fully or partially disordered, depending on the amount of intrinsically disordered regions (IDRs). It has been known that IDPs are abundant in eukaryotic proteins, localized preferentially in the nucleus, and play crucial roles in biological processes, signal transduction and transcriptional regulation. To understand nature of IDPs, we have developed an IDP database and a computer system to predict IDRs.

The IDEAL database

IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments.

Fukuchi, S., Sakamoto, S., Nobe, Y., Murakami, D. S., Amemiya, T., Hosoda, K., Koike, R., Hiroaki, H., and Ota, M.* IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. Nucleic Acids Res. 40(D1) D507-D511 (2012).

Fukuchi, S., Sakamoto, S., Nobe, Y., Murakami, D. S., Amemiya, T., Hosoda, K., Koike, R., Hiroaki, H., and Ota, M. IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners. Nucleic Acids Res. D1, D320 – D325 (2014).

The DICHOT system

The DICHOT system predicts IDRs and structural domains (SDs) with an amino acid sequence as an input. In contrast to other available ID prediction programs that merely identify likely ID regions, the DICHOT system classifies the entire protein sequence into SDs and IDRs.

Fukuchi, S, Hosoda, K. Homma, K., Gojobori, T. and Nishikawa, K. Binary classification of protein molecules into intrinsically disordered and ordered segments. BMC Structural Biology 11 29 (2011).

Fukuchi, S, Homma, K., Minezaki, Y., Gojobori, T. and Nishikawa, K. Development of an Accurate Classification system of Proteins into Structured and Unstructured Regions that Uncovers Novel Structural Domains: Its Application to Human Transcription Factors. BMC Structural Biology 9 26 (2009).