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Processing binding data using an open-source workflow
Journal of Cheminformatics ( IF 8.6 ) Pub Date : 2021-12-11 , DOI: 10.1186/s13321-021-00577-1
Errol L G Samuel 1, 2 , Secondra L Holmes 1, 2 , Damian W Young 1, 2, 3
Affiliation  

The thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There are several approaches that aim to streamline this process, but most involve proprietary software, programming knowledge, or are designed for specific instrument output files. We therefore developed an analysis workflow implemented in the Konstanz Information Miner (KNIME), a free and open-source data analytics platform, which greatly streamlined our data processing timeline for 384-well plates. The implementation is code-free and freely available to the community for improvement and customization to accommodate a wide range of instrument input files and workflows.

中文翻译:

使用开源工作流处理绑定数据

热位移测定 (TSA)——也称为差示扫描荧光法 (DSF)、thermofluor 和 Tm 位移——是基于片段的配体发现 (FBLD) 检测蛋白质-配体相互作用的最流行的生物物理筛选技术之一。通过比较存在和不存在配体的靶蛋白的热稳定性,可以确定潜在的结合物。该技术易于设置,蛋白质消耗低,可在大多数实时聚合酶链反应 (PCR) 仪器上运行。虽然数据分析原则上很简单,但当筛选涉及多个 96 或 384 孔板时,它变得繁琐且耗时。有几种方法旨在简化这个过程,但大多数涉及专有软件、编程知识、或专为特定仪器输出文件而设计。因此,我们开发了在 Konstanz Information Miner (KNIME) 中实施的分析工作流,这是一个免费的开源数据分析平台,极大地简化了我们对 384 孔板的数据处理时间表。该实现是无代码的,社区可以免费使用以进行改进和定制,以适应各种仪器输入文件和工作流程。
更新日期:2021-12-11
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