VSPrep: A General KNIME Workflow for the Preparation of Molecules for Virtual Screening
VSPrep: A General KNIME Workflow for the Preparation of Molecules for Virtual Screening
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DOI：
10.1002/minf.201700023
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发表时间：
2017-10-01
影响因子：
3.6
通讯作者：
Bonnet, Pascal
中科院分区：
文献类型：
--
作者：
Gally, Jose-Manuel;Bourg, Stephane;Bonnet, Pascal
在过去的几十年里，虚拟筛选已被证明是识别新的生物活性化合物的宝贵资产。绝大多数常用技术可以分为三个步骤：预处理数据集，即小分子（配体）和最终较大的分子（受体），执行方法并最终分析结果。因此，配体的制备是常用的虚拟筛选方法如蛋白质-配体对接、相似性或药效团搜索成功的关键步骤。我们在这里提出了一个新的工作流程，VSPrep，用于小分子的预处理;它基于学术界免费访问的工具，并集成在KNIME平台中。它可以用来执行几个化学信息学任务，如分子数据库清理，互变异构体和立体异构体计数，重点库设计和构象生成。此外，结果的图形报告作为方便的分析工具提供给用户。
Over the past decades, virtual screening has proved itself to be a valuable asset to identify new bioactive compounds. The vast majority of commonly used techniques can be described in three steps: pre-processing the dataset i.e. small (ligands) and eventually larger (receptors) molecules, execute the method and finally analyse the results. Hence, the preparation of ligands is a critical step for success of commonly used virtual screening approaches such as protein-ligand docking, similarity or pharmacophore search. We present here a new workflow, VSPrep, for the pre-processing of small molecules; it is based on freely accessible tools for academics and is integrated within the KNIME platform. It can be used to perform several chemoinformatics tasks such as molecular database cleaning, tautomer and stereoisomer enumeration, focused library design and conformer generation. Additionally, graphical reports of the results are provided to the user as a convenient analysis tool.