BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states.
BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states.
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DOI：
10.1186/1756-0500-4-143
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发表时间：
2011-05-22
影响因子：
1.8
通讯作者：
Shimizu K
中科院分区：
文献类型：
--
作者：
Morita M;Terada T;Nakamura S;Shimizu K
阐明蛋白质的分子识别，例如酶-底物和受体-配体相互作用，是理解生物现象的关键。为了描述这些蛋白质的相互作用，进行与分子识别相关的结构生物信息学研究是很重要的。这些研究需要配体结合和未结合状态之间的蛋白质结构对的数据集。在许多研究中，同一个精心设计和高质量的数据集被反复使用，这刺激了后续相关研究的发展。使用先前构建的数据集，研究人员能够公平地将获得的结果与其他研究的结果进行比较;此外，节省了大量的精力和时间。因此，重要的是要构建一个精致的数据集，将吸引许多研究人员。然而，构建这样的数据集并不是一项简单的任务。我们已经开发了BUDDY系统，该网站旨在支持构建一个数据集，该数据集包括配体结合和未结合状态之间的蛋白质结构对，该数据集广泛用于与分子识别相关的各个领域。除了构建数据集外，BUDDY系统还允许用户通过其未结合状态或其配体搜索配体结合的蛋白质结构;并通过特定的受体蛋白质搜索配体。BUDDY系统接收来自用户的输入，作为单个条目或由配体结合状态蛋白质结构、未结合状态蛋白质结构或配体的列表组成的数据集，并向用户返回配体结合状态和相应未结合状态之间的蛋白质结构对的列表。本网站是为那些不仅从事结构生物信息学研究，而且从事实验研究的研究人员而设计的。BUDDY系统可在网上免费获得。
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.