Development of ultra-fast comparison method of protein local structures towards the prediction of ligand-binding sites

2014 Fiscal Year Final Research Report

• Project/Area Number: 23500374
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: TOMII KENTARO 独立行政法人産業技術総合研究所, ゲノム情報研究センター, 研究チーム長 (40357570)
• Co-Investigator(Renkei-kenkyūsha): TSUDA Koji 東京大学, 大学院新領域創成科学研究科・情報生命科学専攻, 教授 (90357517) ; SHIMIZU Kana 産業技術総合研究所, ゲノム情報研究センター, 主任研究員 (60367050) ; ITO Junichi 医薬基盤研究所, 特任研究員
• Project Period (FY): 2011-04-28 – 2015-03-31
• Keywords: タンパク質 / 基質結合部位 / 機能部位 / 低分子医薬品

Outline of Final Research Achievements

In this study, we have developed a novel method that can perform a large-scale comparison of protein-ligand binding sites by utilizing a coarse-grained representation of binding sites and a fast sorting algorithm. Using the method, we conducted a large-scale all-pairs similarity search for both known and potential binding sites in the PDB, and constructed the database, called PoSSuM, that listed the discovered similar site pairs. PoSSuM has grown to provide information related to 49 million pairs of similar binding sites discovered among 5.5 million known and putative binding sites. For pharmaceutical applications, such as predictions of side effects and drug repositioning, we have provided a new database, PoSSuMds (PoSSuM drug search) to catalog detected known and potential binding sites for approved drug compounds whose assay data were retrieved from ChEMBL.

Free Research Field

生命情報学