Diedrich Konrad, Graef Joel, Schöning-Stierand Katrin, Rarey Matthias
Universität Hamburg, ZBH - Center for Bioinformatics, 20146 Hamburg, Germany.
Bioinformatics. 2021 Apr 20;37(3):424-425. doi: 10.1093/bioinformatics/btaa693.
The searching of user-defined 3D queries in molecular interfaces is a computationally challenging problem that is not satisfactorily solved so far. Most of the few existing tools focused on that purpose are desktop based and not openly available. Besides that, they show a lack of query versatility, search efficiency and user-friendliness. We address this issue with GeoMine, a publicly available web application that provides textual, numerical and geometrical search functionality for protein-ligand binding sites derived from structural data contained in the Protein Data Bank (PDB). The query generation is supported by a 3D representation of a start structure that provides interactively selectable elements like atoms, bonds and interactions. GeoMine gives full control over geometric variability in the query while performing a deterministic, precise search. Reasonably selective queries are processed on the entire set of protein-ligand complexes in the PDB within a few minutes. GeoMine offers an interactive and iterative search process of successive result analyses and query adaptations. From the numerous potential applications, we picked two from the field of side-effect analyze showcasing the usefulness of GeoMine.
GeoMine is part of the ProteinsPlus web application suite and freely available at https://proteins.plus.
Supplementary data are available at Bioinformatics online.
在分子界面中搜索用户定义的3D查询是一个计算上具有挑战性的问题，目前尚未得到令人满意的解决。少数现有的专注于该目的的工具大多基于桌面且未公开可用。除此之外，它们还缺乏查询通用性、搜索效率和用户友好性。我们通过GeoMine解决了这个问题，GeoMine是一个公开可用的网络应用程序，为从蛋白质数据库（PDB）中包含的结构数据衍生的蛋白质-配体结合位点提供文本、数值和几何搜索功能。查询生成由起始结构的3D表示支持，该表示提供了诸如原子、键和相互作用等可交互选择的元素。GeoMine在执行确定性精确搜索时，能对查询中的几何变异性进行全面控制。合理的选择性查询可在几分钟内在PDB中的整个蛋白质-配体复合物集合上进行处理。GeoMine提供了一个交互式和迭代式的搜索过程，包括连续的结果分析和查询调整。在众多潜在应用中，我们从副作用分析领域挑选了两个来展示GeoMine的实用性。
GeoMine是ProteinsPlus网络应用程序套件的一部分，可在https://proteins.plus上免费获取。
补充数据可在《生物信息学》在线获取。
