D554–D558 Nucleic Acids Research, 2012, Vol. 40, Database issue doi:10.1093/nar/gkr966 Published online 10 November 2011 PSCDB: a database for protein structural change upon ligand binding Takayuki Amemiya 1 , Ryotaro Koike 1 , Akinori Kidera2,3,* and Motonori Ota1,* 1Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, 2Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 and 3Computational Science Research Program, Riken, 2-1 Hirosawa, Wako 351-0198, Japan Received August 11, 2011; Revised October 6, 2011; Accepted October 16, 2011 ABSTRACT Proteins are flexible molecules that undergo struc- tural changes to function. The Protein Data Bank contains multiple entries for identical proteins deter- mined under different conditions, e.g. with and with- out a ligand molecule, which provides important information for understanding the structural changes related to protein functions. We gathered 839 protein structural pairs of ligand-free and ligand-bound states from monomeric or homo- dimeric proteins, and constructed the Protein Structural Change DataBase (PSCDB). In the data- base, we focused on whether the motions were coupled with ligand binding. As a result, the protein structural changes were classified into seven classes, i.e. coupled domain motion (59 structural changes), independent domain motion (70), coupled local motion (125), independent local motion (135), burying ligand motion (104), no significant motion (311) and other type motion (35). PSCDB provides lists of each class. On each entry page, users can view detailed information about the mo- tion, accompanied by a morphing animation of the structural changes. PSCDB is available at http:// idp1.force.cs.is.nagoya-u.ac.jp/pscdb/. INTRODUCTION Proteins are inherently ﬂexible molecules, since their folded structures are mainly stabilized by non-covalent interactions. Although a static crystal structure provides an impression of a single rigid state, proteins exist in a range of structures. The Protein Data Bank (PDB) (1,2) contains a number of redundant entries for identical proteins with structures determined under different condi- tions, e.g. with and without a ligand molecule. These structures represent a range of variations in the native structures that are associated with their molecular func- tions (3–19). Recently, we collected the structural changes of proteins, represented by pairs of ligand-free and ligand- bound structures of identical proteins, to analyze whether the motions were coupled with ligand binding (20). The protein motions were classiﬁed into domain motions and local motions, depending on the size of the moving por- tions, and we identiﬁed the coupling with ligand binding by examining the relative positions between the lig- and binding sites and the moving portions (20). Here, we have constructed the Protein Structural Change DataBase (PSCDB), which presents the detailed results of the analysis, i.e. the classiﬁcations of protein structural changes focusing on the coupling between protein motions and ligand binding. PSCDB will be an important resource to explore the essential motions for protein functions. A few databases on protein structural changes, such as the database of macromolecular movements (21,22) and the non-redundant database of protein domain move- ments (23,24), are presently available. However, these databases have not focused on the causes of the structural changes. As a result, the databases contain various protein motions that are not necessarily essential to protein func- tions or artifacts due to crystal packing. Recently, Qi and Hayward (15) developed a database of protein motions induced by ligand binding, but they considered only do- main motions in enzymes. PSCDB covers all kinds of protein motions, including not only domain motions of enzymes but also other types of motions seen in enzymes and non-enzymes. METHODS Data in PSCDB Because the process of the dataset construction was pre- viously described (20) in detail, we will brieﬂy outline it here. We collected representative 839 structural changes of monomeric or homo-dimeric proteins, which are the pairs of the ligand-free and ligand-bound structures satisfying *To whom correspondence should be addressed. Email: kidera@tsurumi.yokohama-cu.ac.jp Correspondence may also be addressed to Motonori Ota. Email: mota@is.nagoya-u.ac.jp The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.