D544 Nucleic Acids Research, 2012, Vol. 40, Database issue Figure 1. Categorization of 14 million obtained pairs. (A) 9 625 132 pairs (66%) comprised only known ligand-binding sites, whereas 4 930 925 pairs (34%) comprised a known ligand-binding site and a putative site. (B) Undeﬁned pairs were 7 042 317 (49%). The remaining pairs were categorized into two groups: 5 540 245 pairs of homologs (38%) and 1 973 495 pairs of analogs (13%). Figure 2. Submission form of PoSSuM. PDB ID and HET code of ligand should be speciﬁed for SearchK; PDB ID is required for SearchP. Input: submit a known ligand-binding site or a whole protein structure The required inputs for SearchK are PDB ID (e.g. 1DJQ) of a protein structure and the HET code (e.g. ADP, CA, or K) of a ligand bound to the structure (Figure 2). A protein structure frequently contains multiple ligands with the same HET code. Users can specify the ligand by selecting ‘Chain ID’. Otherwise, all ligands with a name corresponding to the HET code the users selected are regarded as query sites. Users can select a target data set from known ligand-binding sites, putative-binding sites, or both. The only required input for SearchP is a PDB ID of interest. The potential binding pockets of the query structure will be searched against the known ligand-binding sites. For advanced search options such as similarity thresholds, please refer to our website. Output: report a list of similar binding sites Once the query is posted, a summary of the query is dis- played at the top of the result page (Figure 3). Sites are listed and sorted in descending order of aligned length if similar binding sites are detected against the query. Information related to each hit (similar binding site) is presented in a row in the list. The rows involved with known ligand-binding sites are shown with a blue back- ground; putative ones are green. The ﬁrst column shows the superposition of the query site to the hit. The second to fourth columns, respectively, show the PDB ID of the structure, the name of the bound ligand and the Chain ID of the ligand. Regarding putative sites, the name of the bounded ligand is simply displayed as ‘PRB’. The ﬁfth to eighth columns show similarity/dissimilarity values such as cosine similarity, P-value [based on our empirical