D360–D364 Nucleic Acids Research, 2009, Vol. 37, Database issue doi:10.1093/nar/gkn659 Published online 4 October 2008 PiSite: a database of protein interaction sites using multiple binding states in the PDB Miho Higurashi1, Takashi Ishida1 and Kengo Kinoshita1,2,* 1Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 and 2Bioinformatics Research and Development, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan Received August 15, 2008; Revised September 19, 2008; Accepted September 21, 2008 ABSTRACT The vast accumulation of protein structural data has now facilitated the observation of many differ- ent complexes in the PDB for the same protein. Therefore, a single protein complex is not sufficient to identify their interaction sites, especially for proteins with multiple binding states or different partners, such as hub proteins. PiSite is a database that provides protein–protein interaction sites at the residue level with consideration of multiple com- plexes at the same time, by mapping the binding sites of all complexes containing the same protein in the PDB. PiSite provides easy web interfaces with an interactive viewer working with typical web browsers, and the different binding modes can be checked visually. All of the information can also be downloaded for further analyses. In addition, PiSite provides a list of proteins with multiple binding partners and multiple binding states, as well as up-to-date statistics of protein–protein interfaces. PiSite is available at http://pisite.hgc.jp INTRODUCTION Protein–protein interactions are fundamental for proteins to exert their biological functions, and the molecular inter- actions of proteins can be understood by observing the 3D structure of their complexes. Therefore, many eﬀorts have been made to solve complex structures experimentally, and a large number of structures are now available in the Protein Data Bank (PDB) (1). As a result of the vast accumulation of structural data from several genomic proj- ects (2), we can now estimate the structural changes of pro- teins (3), the evolution of homo-oligomerization states (4,5) and the changes in protein–protein interactions (6) by analyzing all of the structures in the PDB simultaneously. The structural characteristics of protein–protein inter- action sites have been extensively studied (7,8), and the knowledge has been used for the prediction of binding sites (9–12). For the statistical analyses, one representative is usually selected for each group with similar amino acid sequences. However, some proteins, called hub proteins (13), interact with several kinds of diﬀerent proteins, and thus one representative complex is not suﬃcient to describe all of the interfaces of a hub protein. For the identiﬁcation of all of the binding sites of a hub protein, all of the complexes within the PDB should be considered at the same time. Protein structures often consist of structural domains, and protein interactions can sometimes be interpreted as domain–domain interactions (14). Therefore, many databases to describe domain–domain interactions have been developed [3did (15), DIMA2 (15) and DOMINE (16)], and networks of domain interactions have been constructed. In these databases, large-scale interaction networks are the main focus, and the residue-level inter- actions are not described. On the other hand, for better understanding the molecular interactions of protein domains, SCOPPI (17) and iPFAM (18) provide residue- level information about the interacting domains, but the interacting residues are provided for each pair of interact- ing domains (iPfam) or a multiple alignment in the family with interface classiﬁcation (SCOPPI), and thus it is diﬃ- cult to observe several diﬀerent binding modes of proteins with multiple partners. In addition, SCOPPI focuses on the diversity at the family level, while we would like to observe the multiple binding modes for individual pro- teins. In the similar way, PiBase (19) provides detailed physicochemical properties for all the protein complexes in the PDB as a correction of binary relationships. In this article, we describe a new protein–protein inter- action database, PiSite, based on the protein complexes in *To whom correspondence should be addressed. Tel: +81 3 5449 5131; Fax: +81 3 5449 5133; Email: kino@ims.u-tokyo.ac.jp The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.