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.

中文翻译：

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visGReMLIN：基于图挖掘的检测和可视化原子级别的3D蛋白质-配体界面上的保守基序。

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，发展计算方法以支持我们对配体-受体识别过程的理解至关重要，因为这些方法是迈向配体预测，靶标鉴定，发现线索等的重要步骤。本文介绍了visGReMLIN，这是一种Web服务器，它结合了基于图挖掘的策略来检测蛋白质-配体界面上的基序，以及一个交互式平台，可以在蛋白质-配体界面的背景下直观地探索和解释这些基序。为了说明visGReMLIN的潜力，我们进行了两个案例，将我们的策略与先前的实验和计算结果进行了比较。visGReMLIN使我们能够以完全可视的方式检测文献中先前记录的模式。此外，我们在分析的数据集中发现了一些我们认为与蛋白质-配体相互作用有关的基序。我们旨在构建面向视觉分析的Web服务器，以检测和可视化蛋白质-配体界面上的常见基序。visGReMLIN基序可以帮助用户深入了解负责复杂数据集中蛋白质-配体相互作用的关键原子/残基。