Department of Environmental Science, Computer Science and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy.
Department of Molecular Science and Nanosystems, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy.
BMC Bioinformatics. 2023 Sep 11;24(1):336. doi: 10.1186/s12859-023-05466-y.
Residue Interaction Networks (RINs) map the crystallographic description of a protein into a graph, where amino acids are represented as nodes and non-covalent bonds as edges. Determination and visualization of a protein as a RIN provides insights on the topological properties (and hence their related biological functions) of large proteins without dealing with the full complexity of the three-dimensional description, and hence it represents an invaluable tool of modern bioinformatics.
We present RINmaker, a fast, flexible, and powerful tool for determining and visualizing RINs that include all standard non-covalent interactions. RINmaker is offered as a cross-platform and open source software that can be used either as a command-line tool or through a web application or a web API service. We benchmark its efficiency against the main alternatives and provide explicit tests to show its performance and its correctness.
RINmaker is designed to be fully customizable, from a simple and handy support for experimental research to a sophisticated computational tool that can be embedded into a large computational pipeline. Hence, it paves the way to bridge the gap between data-driven/machine learning approaches and numerical simulations of simple, physically motivated, models.
残基相互作用网络（RINs）将蛋白质的晶体描述映射到一个图中，其中氨基酸表示为节点，非共价键表示为边。确定和可视化蛋白质的 RIN 提供了关于拓扑性质（因此是它们相关的生物学功能）的见解，而无需处理三维描述的全部复杂性，因此它代表了现代生物信息学的宝贵工具。
我们提出了 RINmaker，这是一种快速、灵活且功能强大的工具，用于确定和可视化包括所有标准非共价相互作用的 RIN。RINmaker 作为跨平台和开源软件提供，可以作为命令行工具使用，也可以通过 Web 应用程序或 Web API 服务使用。我们对其效率进行了基准测试，并提供了明确的测试来展示其性能和正确性。
RINmaker 旨在完全可定制，从简单易用的实验研究支持到可嵌入到大型计算管道中的复杂计算工具。因此，它为弥合数据驱动/机器学习方法与简单、物理驱动的数值模拟之间的差距铺平了道路。
