D362 Nucleic Acids Research, 2009, Vol. 37, Database issue partners were grouped by sequence identity, and the number of groups was used as the number of binding partners shown in PiSite. Here, we regarded two proteins as being in the same group, if they have >30% sequence identity and >50% coverage of the smaller chain. Each binding state of a protein was deﬁned as the combination and the number of binding partners appeared in the PDB. For example, when we consider the binding state of pro- tein A with the complexes A–B and A–B–C in the PDB, then the number of binding states of protein A is two. If we have another complex A–B–B, then the number of binding states is three, because the number of binding partner B is diﬀerent from that in the complex A–B. It should be noted that the similarities between binding sites are not considered explicitly in our approach, thus the number of binding state can be smaller than that of the binding modes, while we used all complexes for the residue mapping to get the comprehensive mapping. The deﬁnitions of binding states and binding partners are virtually same as those used in Higurashi et al. (6), but we modiﬁed the original protocol to handle all PDB entries in PiSite, as described. Definition of sociable proteins We basically followed the sociable protein deﬁnition by Higurashi et al. (6). However, since automated processes are required in this study and we could not apply manual curation, we used a stricter deﬁnition. We deﬁned proteins with three or more binding states and three or more bind- ing partners as sociable proteins. We excluded proteins with more than 10 chains in a single PDB entry as super- molecules. In addition, we also excluded proteins with four or fewer similar proteins in the data set. This last condition is to ensure the reliability of sociable protein identiﬁcations. If the number of similar proteins is too small, then this deﬁnition may contain some errors. CONTENTS OF PiSite The main content of the PiSite is an interactive view of the multiple binding states, and we refer to the corresponding web page as the interaction viewer. The interaction viewer (Fig. 2) shows all binding states appearing in the PDB, and is prepared for each protein chain. It consists of four parts: title table including a link to UniprotKB (25), a molecule viewer, a binding state viewer and a download menu. The title table contains brief descriptions of the protein chain and the numbers of similar proteins, binding states and binding partners. The molecule viewer shows the protein, colored accord- ing to the number of binding partners for each residue in default. The amino acid sequence is also colored according to the same procedure, and is shown just below the viewer. The position of each amino acid can be checked by click- ing a residue in the sequence, which changes the speciﬁed residue into a CPK model (Fig. 2). Visualization of the molecule was done by jV [formally known as pdbjviewer (26)], and thus the view of the molecule can be interac- tively rotated and translated by mouse operations, and the residue position can be inspected by clicking the residue on the screen. More detailed options for jV are also avail- able, by opening the option screen at the top of the mole- cule viewer (Fig. 2). The binding state viewer shows a diﬀerent binding state of the proteins, by communicating with the molecule viewer. By switching to a diﬀerent binding state with the radio button, the complex structure is shown in the mole- cule viewer with the same color as the background of the partner name. It may be noteworthy that two or more protein names appear as binding partners as in the cases of the 9th and 10th binding states in Fig. 2, which means that the binding state contains three or more chains, including the chain under consideration. The names of the binding partners are taken from the DBREF record in the PDB entry. All of the data obtained after mapping the similar proteins can be downloaded in a ﬂat ﬁle or XML format. The format is described in the download page. OTHER CONTENTS PiSite also provides a list of sociable proteins, which are proteins with multiple binding states and multiple binding partners. In our original paper, the number of sociable proteins was 86 (6), where only the structures with a reso- lution of 3.0 A˚ or better were selected from the PDB as of July 2006. In contrast, the number of nonredundant socia- ble proteins in the current release of PiSite is 102, where the redundancies were eliminated by selecting one repre- sentative from 30% identity sequence clusters. The diﬀer- ence arises mainly from the date of the PDB and the inclusion of NMR data in PiSite. On the statistics page, we also show some statistical analyses of amino acid occurrence in the protein–protein interfaces based on the latest release of PiSite, which will be useful to develop statistical parameters to evaluate the likelihood of protein–protein interfaces. All of the raw data are also available from the statistics page for further analyses. ACCESS TO EACH ENTRY, WITH AN EXAMPLE PiSite provides two diﬀerent ways to access each entry. The ﬁrst way is access from a compiled list. PiSite provides a list of representative sociable proteins and supermole- cules, as mentioned above. These lists contain links for the entries and the user can access them by clicking the links. The other way is to search by sequence or keywords. Both sequence and keyword searches are available, through the search form on the top page. A sequence search requires amino acid sequence of a protein chain as an input and is performed by using BLAST. A more general search is by keywords. If the user wants to check the PiSite entry for Ras p21 proteins, for example, then the user can search ‘RAS p21’ as a keyword. As a result, the search results, including a moleculer description of the target and infor- mation about the number of binding states and partners are obtained. Each PiSite entry can be accessed from links in a search result page. In this case, the user can access the PiSite entry of the hRas P21 protein (PDBID: 121p, chain A) by clicking the link of the top hit of the search