ePharmer: An integrated and graphical software for pharmacophore-based virtual screening,Journal of Computational Chemistry

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ePharmer: An integrated and graphical software for pharmacophore-based virtual screening
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2021-08-19 , DOI: 10.1002/jcc.26743
Yuxia Mao ₁ , Shiliang Li ₂ , Bojie Gong ₃ , Luhua Lai ₄ , Gaoqi He ₁ , Honglin Li ₂

Affiliation

Pharmacophore-based virtual screening (VS) has emerged as an efficient computer-aided drug design technique when appraising multiple ligands with similar structures or targets with unknown crystal structures. Current pharmacophore modeling and analysis software suffers from inadequate integration of mainstream methods and insufficient user-friendly program interface. In this study, we propose a stand-alone, integrated, graphical software for pharmacophore-based VS, termed ePharmer. Both ligand-based and structure-based pharmacophore generation methods were integrated into a compact architecture. Fine-grained modules were carefully organized into the computing, integration, and visualization layers. Graphical design covered the global user interface and specific user operations including editing, evaluation, and task management. Metabolites prediction analysis with the chosen VS result is provided for preselection of wet experiments. Moreover, the underlying computing units largely adopted the preliminary work of our research team. The presented software is currently in client use and will be released for both professional and nonexpert users. Experimental results verified the favorable computing capability, user convenience, and case performance of the proposed software.

中文翻译：

ePharmer：用于基于药效团的虚拟筛选的集成图形软件

在评估具有相似结构的多个配体或具有未知晶体结构的靶标时，基于药效团的虚拟筛选 (VS) 已成为一种有效的计算机辅助药物设计技术。目前的药效团建模与分析软件存在主流方法整合不足、程序界面人性化不足等问题。在这项研究中，我们提出了一个独立的、集成的、基于药效团的 VS 的图形软件，称为 ePharmer。基于配体和基于结构的药效团生成方法都集成到一个紧凑的架构中。细粒度的模块被精心组织成计算、集成和可视化层。图形设计涵盖了全局用户界面和特定的用户操作，包括编辑、评估和任务管理。为湿实验的预选提供具有所选 VS 结果的代谢物预测分析。此外，底层计算单元很大程度上采用了我们研究团队的前期工作。所展示的软件目前供客户使用，将面向专业用户和非专家用户发布。实验结果验证了所提软件良好的计算能力、用户便利性和案例性能。

更新日期：2021-10-09

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