D556 Nucleic Acids Research, 2012, Vol. 40, Database issue Figure 2. Seven classes. The names, abbreviations, and numbers of protein structural changes of the seven classes are shown on the top-page of PSCDB, with the cartoon icons depicting each motion. User interface Users can view the list table of structural changes by clicking the icon of classiﬁcation (Figure 2), or access the list table and the gallery of all entries by clicking the left box on the top-page. In the list table, the serial identiﬁer, the PSCDB identiﬁer (PSCID), is labeled on the individual structural change together with the protein name, the two PDBIDs (ligand-free and ligand-bound forms) and the ligand name(s). The six digit number shown in the right column in the list table indicates, from the ﬁrst to the sixth digit, the number of components of motion for the coupled domain motion, the number for the independent domain motion, the number for the coupled local motion, the number for the independent local motion, the number of domains exhibiting the burying ligand motion, and the number of domains with ligand molecules situated on the protein surface, respectively. The last number is frequently related to the class of no signiﬁcant motion. PSCDB also provides a search tool at the top-right corner of each page. Users can search for ‘protein name’ or ‘PDBID’. From the list table or the gallery, users can access the summary page of each protein structural change. As an example, the structural change of the hypothetical oxido- reductase YIAK (32) is shown in Figure 3. This protein contains two components of motion, which were both classiﬁed as coupled domain motion. The PSCID is thus CD.1 ([1] in Figure 3). The PDB structures representing the motion are provided in the ‘PDB’ box [2]. To visualize the motion, the three rigid domains (blue, green, and red) and the ligand molecules (spheres) are illustrated in the upper right panel [3]. By clicking the ‘animation’ button [4], morphing animation can be viewed through JMOL (33). The predicted domain motion using the linear re- sponse theory (20,34,35) can also be viewed by clicking the ‘PNG image’ button [5]. If a target protein is an enzyme, then the enzyme commission number and the in- formation about the catalytic sites are shown in the ‘func- tion’ box [6]. The bound-ligand molecule is provided in the ‘ligand’ box [7]. The details of the motions are summarized in the ‘segments’ box [8]. Future directions In PSCDB, the structural changes are presented only for representative proteins of the SCOP families. The repre- sentative protein was selected as the pair of ligand-free and ligand-bound structures of an identical protein with the largest RMSD value in each protein family (20). However, the largest motion does not necessarily repre- sent the dominant motion of the protein family. Therefore, we will examine all pairs of ligand-free and ligand-bound structures of an identical protein, and ana- lyze the ensemble of protein motions in the protein family. We will also develop an automated pipeline to analyze and classify protein structural changes. Using this pipeline, PSCDB can be automatically updated when new PDB