Water and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X-ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein-protein or protein-ligand interactions, as well as conserved water-binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.

中文翻译：

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DRoP：自动检测蛋白质上保守的溶剂结合位点。

水和配体的结合在蛋白质的结构和功能中起着至关重要的作用，但是它们的结合位点和重要性很难先验地预测。多重溶剂晶体结构（MSCS）是一种方法，可以在独特的溶剂环境中解析几种X射线晶体结构，其中有机分子充当蛋白质表面探针的位置，以进化出与配体结合的位置，而第一个水合壳基本上保持不变。当叠加时，这些结构包含有关蛋白质-蛋白质或蛋白质-配体相互作用的热点以及随溶剂性质变化而保留的保守的水结合位点的大量信息。对这些信息的优化挖掘需要可靠的结构数据和一致，客观的分析工具。开发了相关溶剂位置（DRoP）的检测功能，以自动组织和排列给定结构集中的水或有机小分子结合位点。鉴于任何蛋白质的多种结构都独立于MSCS方​​法，它是一种灵活的工具，也可以用于节约用水分析。DRoP输出是溶剂位点的HTML格式列表，这些溶剂位点在该结构集内按其种群中的保守性排序，并带有重新编号和重新着色的PDB文件，以进行可视化和简便分析。在这里，我们介绍了牛胰腺核糖核酸酶A（RNase A）的一组尚未发布的MSCS结构，并将其与已发布的结构一起使用以说明DRoP的功能。