title: PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.
abstract: PoSSuM (http://possum.cbrc.jp/PoSSuM/) is a database for detecting similar small-molecule binding sites on proteins. Since its initial release in 2011, 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. This enlargement of the database is expected to enhance opportunities for biological and pharmaceutical applications, such as predictions of new functions and drug discovery. In this release, we have provided a new service named PoSSuM drug search (PoSSuMds) at http://possum.cbrc.jp/PoSSuM/drug_search/, in which we selected 194 approved drug compounds retrieved from ChEMBL, and detected their known binding pockets and pockets that are similar to them. Users can access and download all of the search results via a new web interface, which is useful for finding ligand analogs as well as potential target proteins. Furthermore, PoSSuMds enables users to explore the binding pocket universe within PoSSuM. Additionally, we have improved the web interface with new functions, including sortable tables and a viewer for visualizing and downloading superimposed pockets.
authors.affiliation: Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan k-tomii@aist.go.jp.
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Ito
authors.affiliation: Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan Drug Discovery Informatics Group, System Solution Division, Level Five Co. Ltd., Shiodome Shibarikyu Bldg., 1-2-3 Kaigan, Minato-ku, Tokyo 105-0022, Japan.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Ikeda
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Kazunori
authors.initials: K
authors.lastname: Yamada
authors.affiliation: Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan k-tomii@aist.go.jp.
authors.forename: Kenji
authors.initials: K
authors.lastname: Mizuguchi
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan k-tomii@aist.go.jp.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Tomii
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D015195:Drug Design; D020407:Internet; D008024:Ligands; D004364:Pharmaceutical Preparations / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D004364:Pharmaceutical Preparations; D011506:Proteins