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Open Access Technical Note

BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states

Mizuki Morita12*, Tohru Terada3, Shugo Nakamura4 and Kentaro Shimizu24

Author Affiliations

1 Department of Fundamental Research, National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito Asagi, Ibaraki, Osaka 567-0085, Japan

2 Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan

3 Agricultural Bioinformatics Research Unit, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan

4 Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan

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BMC Research Notes 2011, 4:143  doi:10.1186/1756-0500-4-143

Published: 22 May 2011



Elucidating molecular recognition by proteins, such as in enzyme-substrate and receptor-ligand interactions, is a key to understanding biological phenomena. To delineate these protein interactions, it is important to perform structural bioinformatics studies relevant to molecular recognition. Such studies require a dataset of protein structure pairs between ligand-bound and unbound states. In many studies, the same well-designed and high-quality dataset has been used repeatedly, which has spurred the development of subsequent relevant research. Using previously constructed datasets, researchers are able to fairly compare obtained results with those of other studies; in addition, much effort and time is saved. Therefore, it is important to construct a refined dataset that will appeal to many researchers. However, constructing such datasets is not a trivial task.


We have developed the BUDDY-system, a web site designed to support the building of a dataset comprising pairs of protein structures between ligand-bound and unbound states, which are widely used in various areas associated with molecular recognition. In addition to constructing a dataset, the BUDDY-system also allows the user to search for ligand-bound protein structures by its unbound state or by its ligand; and to search for ligands by a particular receptor protein.


The BUDDY-system receives input from the user as a single entry or a dataset consisting of a list of ligand-bound state protein structures, unbound state protein structures, or ligands and returns to the user a list of protein structure pairs between the ligand-bound and the corresponding unbound states. This web site is designed for researchers who are involved not only in structural bioinformatics but also in experimental studies. The BUDDY-system is freely available on the web.