Interaction between protein and ligands are ubiquitous in a biological cell, and understanding these interactions at the atom level in protein–ligand complexes is crucial for structural bioinformatics and drug discovery. Here, we present a web-based protein–ligand interaction application named Ligand Binding Site Comparison (LiBiSCo) for comparing the amino acid residues interacting with atoms of a ligand molecule between different protein–ligand complexes available in the Protein Data Bank (PDB) database. The comparison is performed at the ligand atom level irrespectively of having binding site similarity or not between the protein structures of interest. The input used in LiBiSCo is one or several PDB IDs of protein–ligand complex(es) and the tool returns a list of identified interactions at ligand atom level including both bonded and non-bonded interactions. A sequence profile for the interaction for each ligand atoms is provided as a WebLogo. The LiBiSco is useful in understanding ligand binding specificity and structural promiscuity among families that are structurally unrelated. The LiBiSCo tool can be accessed through https://albiorix.bioenv.gu.se/LiBiSCo/HomePage.py.

中文翻译：

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配体结合位点比较 — LiBiSCo — 一种基于网络的工具，用于分析蛋白质和配体之间的相互作用，以探索活性位点内的氨基酸特异性

蛋白质和配体之间的相互作用在生物细胞中无处不在，在蛋白质-配体复合物的原子水平上理解这些相互作用对于结构生物信息学和药物发现至关重要。在这里，我们提出了一个名为 Ligand Binding Site Comparison (LiBiSCo) 的基于网络的蛋白质-配体相互作用应用程序，用于比较蛋白质数据库 (PDB) 数据库中可用的不同蛋白质-配体复合物之间的氨基酸残基与配体分子的原子相互作用. 比较是在配体原子水平上进行的，无论感兴趣的蛋白质结构之间是否具有结合位点相似性。LiBiSCo 中使用的输入是一个或多个蛋白质-配体复合物的 PDB ID，该工具返回一个在配体原子水平上识别的相互作用列表，包括键合和非键合相互作用。每个配体原子的相互作用的序列谱以 WebLogo 的形式提供。LiBiSco 有助于了解结构上不相关的家族之间的配体结合特异性和结构混杂。LiBiSCo 工具可以通过 https://albiorix.bioenv.gu.se/LiBiSCo/HomePage.py 访问。