Drug discovery is a challenging and expensive field. Hence, novel in silico tools have been developed in early discovery stage to identify and prioritize novel molecules with suitable physicochemical properties. In many in silico drug design projects, molecular databases are screened by virtual screening tools to search for potential bioactive molecules. The preparation of the molecules is therefore a key step in the success of well-established techniques such as docking, similarity or pharmacophore searching. We review here the lists of several toolkits used in different steps during the cleaning of molecular databases, integrated within a KNIME workflow. During the first step of the automatic workflow, salts are removed, and mixtures are split to get one compound per entry. Then compounds with unwanted features are filtered. Duplicated entries are then deleted while considering stereochemistry. As a compromise between exhaustiveness and computational time, most distributed tautomers at physiological pH are computed. Additionally, various flags are applied to molecules by using either classical molecular descriptors, similarity search to known libraries or substructure search rules. Moreover, stereoisomers are enumerated depending on the unassigned chiral centers. Then, three-dimensional coordinates, and optionally conformers, are generated. This workflow has been already applied to several drug design projects and can be used for molecular database preparation upon request.

药物发现是一个充满挑战且昂贵的领域。因此，在早期发现阶段已经开发了新颖的计算机模拟工具，以鉴定具有合适的物理化学性质的新颖分子并对其进行优先排序。在许多计算机药物设计项目中，通过虚拟筛选工具筛选分子数据库以搜索潜在的生物活性分子。因此，分子的制备是成功建立的技术（如对接，相似性或药效基团搜索）成功的关键步骤。我们在这里回顾了KNIME工作流程中集成的分子数据库清洗过程中不同步骤所使用的几种工具包的列表。在自动工作流程的第一步中，将盐去除，然后将混合物分开以使每次输入得到一种化合物。然后过滤具有不想要特征的化合物。然后在考虑立体化学的同时删除重复的条目。作为穷举性和计算时间之间的折衷，可以计算生理pH下大多数分布的互变异构体。另外，通过使用经典分子描述符，与已知库的相似性搜索或子结构搜索规则，可以将各种标记应用于分子。此外，根据未分配的手性中心列举了立体异构体。然后，生成三维坐标，以及可选的构象体。该工作流程已被应用于多个药物设计项目，并可应要求用于分子数据库的制备。通过使用经典分子描述符，与已知库的相似性搜索或子结构搜索规则，可以将各种标记应用于分子。此外，根据未分配的手性中心列举了立体异构体。然后，生成三维坐标，以及可选的构象体。该工作流程已被应用于多个药物设计项目，并可应要求用于分子数据库的制备。通过使用经典分子描述符，与已知库的相似性搜索或子结构搜索规则，可以将各种标记应用于分子。此外，根据未分配的手性中心列举了立体异构体。然后，生成三维坐标，以及可选的构象体。该工作流程已被应用于多个药物设计项目，并可应要求用于分子数据库的制备。