the following criteria: They are X-ray crystalline structures determined with higher than 3.0 A˚ resolution, and the se- quence identity of the pair is >95%, with at least 90% coverage. The oligomeric states of the pair were identiﬁed according to PiQSi (Protein Quaternary Structure Investigation) (25). The representative pairs were selected according to the SCOP (structural classiﬁcation of proteins) family (26), or based on clustering with 40% sequence identity. The representative pairs of ligand-free and ligand-bound structures of monomers and homo-dimers are a dominant part of the structural database: they occupy more than three quarters of the whole set of representative pairs including monomers and all kinds of oligomers. Classiﬁcation of protein motions DynDom (27,28) was applied to the protein structures, regardless of monomeric or dimeric forms, and domain motions were detected. When more than two domains were identiﬁed, the protein structure was divided into the com- ponents of motion, each deﬁned as two neighboring domains exhibiting a domain motion (Figure 1a). Consequently, a protein structure may have one or more components of motion, or simply a single domain exhibit- ing no domain motion. Next, the local motions were identiﬁed in each domain. A local motion was deﬁned as that occurring in a local segment composed of more than ﬁve residues, with a displacement at least four times larger than the median for all residues. When more than one moving local segment was identiﬁed in a domain, the do- main was divided into the components of motion, each composed of the core domain and a moving local segment (Figure 1b). Finally, each component of motion was as- sessed according to whether the motion was coupled with ligand-binding, by examining the relative positions of the ligand binding site and the moving portion. A component Nucleic Acids Research, 2012, Vol. 40, Database issue D555 of motion was designated as ‘coupled’ with ligand-binding if both portions constituting the component of motion con- tacted the ligand molecule in the ligand-bound structure. Otherwise, it was classiﬁed as ‘independent’, or uncoupled. Consequently, the protein structural changes were classi- ﬁed as (i) ‘coupled domain motion’, (ii) ‘independent domain motion’, (iii) ‘coupled local motion’ and (iv) ‘in- dependent local motion.’ In the classiﬁcation of a struc- tural change, the coexistence of domain and local motions in a protein was treated as domain motion, and the coex- istence of coupled and independent motions was treated as coupled motion. The rest of the protein motions, other than the above four classes, were classiﬁed as follows. In the structural change with a small displacement [root-mean-square displacement (RMSD) <1.0 A˚], we considered the protein structure to be signiﬁcantly altered when the ligand molecule was buried inside of the protein core, i.e. the relative accessible surface area (31) of the ligand was >90%. We refer to this type of structural change as (v) ‘burying ligand motion’. We visually checked pocket shapes for ligands and conﬁrmed that it would be impossible to bury the ligand without signiﬁcant structural changes. The other motions with small RMSD values were termed (vi) ‘no signiﬁcant motion’. The rest of the motions are (vii) ‘other type motion’, which are mostly outliers of the deﬁnitions of the domain or local motions, despite of large displace- ments (RMSD > 1.0 A˚). They include ‘domain motion like’, ‘local motion like’ and ‘large plastic motion’ described in detail in the previous work (20). We mainly focused only on the coupled motions (classes 1 and 3) in our previous work (20), but PSCDB presents all motions. This classiﬁcation is shown on the top-page of PSCDB, with the number of proteins classiﬁed into each class (Figure 2). Each class is represented by a code of one or two characters; for example, CD stands for ‘coupled domain motion’. Figure 1. Components of motion in domain and local motions. (a) Superposition of glucokinase structures (PDBIDs: 1q18, 1sz2) (29) on the largest domains (blue/cyan). The three domains are colored green/yellow, blue/cyan and red/magenta. The structure was divided into two components of motion (green/yellow and blue/cyan, and red/magenta and blue/cyan). (b) Superposition of D-alanine:D-alanine ligase structures (PDBIDs: 2fb9, 2zdq) (30) on the core domains (blue/cyan). Two moving local segments (green/yellow and red/magenta) were identiﬁed in the protein motion. The structure was divided into two components of motion (green/yellow and blue/cyan, and red/magenta and blue/cyan).