Department of Computer Science, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil.
Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
BMC Bioinformatics. 2020 Mar 11;21(Suppl 2):80. doi: 10.1186/s12859-020-3347-7.
Interactions between proteins and non-proteic small molecule ligands play important roles in the biological processes of living systems. Thus, the development of computational methods to support our understanding of the ligand-receptor recognition process is of fundamental importance since these methods are a major step towards ligand prediction, target identification, lead discovery, and more. This article presents visGReMLIN, a web server that couples a graph mining-based strategy to detect motifs at the protein-ligand interface with an interactive platform to visually explore and interpret these motifs in the context of protein-ligand interfaces.
To illustrate the potential of visGReMLIN, we conducted two cases in which our strategy was compared with previous experimentally and computationally determined results. visGReMLIN allowed us to detect patterns previously documented in the literature in a totally visual manner. In addition, we found some motifs that we believe are relevant to protein-ligand interactions in the analyzed datasets.
We aimed to build a visual analytics-oriented web server to detect and visualize common motifs at the protein-ligand interface. visGReMLIN motifs can support users in gaining insights on the key atoms/residues responsible for protein-ligand interactions in a dataset of complexes.
蛋白质与非蛋白质小分子配体之间的相互作用在生命系统的生物过程中起着重要作用。因此，开发能够支持我们理解配体-受体识别过程的计算方法至关重要，因为这些方法是进行配体预测、靶点鉴定、先导化合物发现等的重要步骤。本文介绍了 visGReMLIN，这是一个网络服务器，它将基于图挖掘的策略与一个交互式平台相结合，用于在蛋白质-配体界面的背景下可视化地探索和解释这些模式。
为了说明 visGReMLIN 的潜力，我们进行了两个案例研究，在这些案例中，我们的策略与以前实验和计算确定的结果进行了比较。visGReMLIN 允许我们以完全可视化的方式检测到文献中记录的模式。此外，我们还发现了一些我们认为与分析数据集的蛋白质-配体相互作用相关的模式。
我们旨在构建一个面向可视化分析的网络服务器，以检测和可视化蛋白质-配体界面上的常见模式。visGReMLIN 模式可以帮助用户深入了解数据集复合物中负责蛋白质-配体相互作用的关键原子/残基。
