Department of Computer Science, Universidad de Talca, Camino Los Niches Km 1, Curicó, Chile.
Millennium Institute for Foundational Research on Data, Santiago, Chile.
BMC Bioinformatics. 2020 Mar 11;21(Suppl 2):85. doi: 10.1186/s12859-020-3352-x.
In the field of protein engineering and biotechnology, the discovery and characterization of structural patterns is highly relevant as these patterns can give fundamental insights into protein-ligand interaction and protein function. This paper presents GSP4PDB, a bioinformatics web tool that enables the user to visualize, search and explore protein-ligand structural patterns within the entire Protein Data Bank.
We introduce the notion of graph-based structural pattern (GSP) as an abstract model for representing protein-ligand interactions. A GSP is a graph where the nodes represent entities of the protein-ligand complex (amino acids and ligands) and the edges represent structural relationships (e.g. distances ligand - amino acid). The novel feature of GSP4PDB is a simple and intuitive graphical interface where the user can "draw" a GSP and execute its search in a relational database containing the structural data of each PDB entry. The results of the search are displayed using the same graph-based representation of the pattern. The user can further explore and analyse the results using a wide range of filters, or download their related information for external post-processing and analysis.
GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.
在蛋白质工程和生物技术领域，发现和描述结构模式非常重要，因为这些模式可以深入了解蛋白质-配体相互作用和蛋白质功能。本文介绍了 GSP4PDB，这是一个生物信息学网络工具，使用户能够在整个蛋白质数据库中可视化、搜索和探索蛋白质-配体结构模式。
我们提出了基于图的结构模式 (GSP) 的概念，作为表示蛋白质-配体相互作用的抽象模型。GSP 是一个图，其中节点代表蛋白质-配体复合物的实体（氨基酸和配体），边代表结构关系（例如配体-氨基酸的距离）。GSP4PDB 的新颖之处在于一个简单直观的图形界面，用户可以在其中“绘制”一个 GSP，并在包含每个 PDB 条目的结构数据的关系数据库中执行其搜索。搜索结果使用模式的基于图的表示形式显示。用户可以使用各种过滤器进一步探索和分析结果，或下载相关信息进行外部后处理和分析。
GSP4PDB 是一个用户友好且高效的应用程序，可用于搜索和发现新的蛋白质-配体相互作用模式。
