ゲノム情報研究センター[CBRC]

2012年10月19日掲載

　生命医薬情報学連合大会(2012年日本バイオインフォマティクス学会年会、情報計算化学生物学会（CBI学会）年次大会 オミックス医療研究会年会)では、170件ほど発表されるポスターの中から優秀な発表を選び、ベストポスター賞を授与しています。2012年10月15-17日に東京・タワーホール船堀で開催された2012年度生命医薬情報学連合大会のベストポスターとして、独立行政法人産業技術総合研究所生命情報工学研究センター細胞システム解析チーム長の富井 健太郎研究員が著者である以下の発表が選ばれました。

ポスター概要

• タイトル:PoSSuM: A Database for Predicting Protein-Ligand Interactions
• 著者:Kentaro Tomii, Jun-ichi Ito, Yasuo Tabei, Kana Shimizu, Koji Tsuda

　Proteins exhibit their functions through interactions with other molecules (so-called ligands), and their functions can be characterized by their ligand binding sites. Today, a large number of ligand binding sites can be found in the Protein Data Bank (PDB). In addition to these known sites, several computational methods are available for predicting potential ligand binding sites. Exhaustive pairwise comparison of such known and potential ligand binding sites is computationally demanding, but useful in elucidating the biological functions of proteins.
　Recently we proposed an ultrafast alignment-free method that can compare over 1 million ligand binding sites in the PDB [1]. In our method, ligand binding sites are encoded as feature vectors based on their physicochemical and geometric properties. Once ligand binding sites are converted to bit strings, called structural sketches, which is obtained by random projections of feature vectors, a multiple sorting method is used to enumerate all similar pairs in terms of the Hamming distance.
　We provide those results as a relational database, called Pocket Similarity Search using Multiple-sketches (PoSSuM) to compile all similar pairs detected by our method [2]. As the source dataset, we concatenated the following two sets: 226,630 small molecule-binding sites obtained from protein-ligand complexes in the PDB, and 3,134,413 potential ligand binding sites identified using an existing pocket detection algorithm, GHECOM [3]. We applied our method to all-pair similarity searches for the 3.4 million known and potential ligand binding sites. Consequently, we discovered over 24 million similar pairs of binding sites. The database contains all the discovered pairs with annotations of various types such as CATH, SCOP, EC numbers, and Gene Ontology (GO) terms. Therefore, one can easily scrutinize similar ligand binding sites between proteins with different folds or similar sites between enzymes with different EC numbers. One can also browse superpositions of similar sites. Our database is expected to be helpful for predicting ligand interactions and rapid screening of target proteins in drug design.
　The PoSSuM database is available at http://possum.cbrc.jp/PoSSuM/

[1] Ito, J., Tabei, Y., Shimizu, K., Tomii, K., and Tsuda, K., PDB-scale analysis of known and putative ligand binding sites with structural sketches, Proteins, 80:747-763, 2012.
[2] Ito, J., Tabei, Y., Shimizu, K., Tsuda, K., and Tomii, K., PoSSuM: a database of similar protein-ligand binding pockets, Nucleic Acids Research, 40:D541-D548, 2012.
[3] Kawabata, T., Detection of multi-scale pockets on protein surfaces using mathematical morphology, Proteins, 78:1195-1121, 2010.

写真：授賞式の様子

　表彰式では、CBI学会大会副委員長の山村 雅幸先生より賞状を授与され、連合大会参加者から多くの祝福と激励をいただきました。