Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kasiska Division of Health Sciences , Idaho State University , Meridian , Idaho 83642 , United States.
J Chem Inf Model. 2019 Jan 28;59(1):18-24. doi: 10.1021/acs.jcim.8b00633. Epub 2018 Nov 16.
As abundant and user-friendly as computer-aided drug design (CADD) software may seem, there is still a large underserved population of biomedical researchers around the world, particularly those with no computational training and limited research funding. To address this important need and help scientists overcome barriers that impede them from leveraging CADD in their drug discovery work, we have developed ezCADD, a web-based CADD modeling environment that manifests four simple design concepts: easy, quick, user-friendly, and 2D/3D visualization-enabled. In this paper, we describe the features of three fundamental applications that have been implemented in ezCADD: small-molecule docking, protein-protein docking, and binding pocket detection, and their applications in drug design against a pathogenic microbial enzyme as an example. To assess user experience and the effectiveness of our implementation, we introduced ezCADD to first-year pharmacy students as an active learning exercise in the Principles of Drug Action course. The web service robustly handled 95 simultaneous molecular docking jobs. Our survey data showed that among the 95 participating students, 97% completed the molecular docking experiment on their own at least partially without extensive training; 88% considered ezCADD easy and user-friendly; 99-100% agreed that ezCADD enhanced the understanding of drug-receptor structures and recognition; and the student experience in molecular modeling and visualization was significantly improved from zero to a higher level. The student feedback represents the baseline data of user experience from noncomputational researchers. It is demonstrated that in addition to supporting drug discovery research, ezCADD is also an effective tool for promoting science, technology, engineering, and mathematics (STEM) education. More advanced CADD applications are being developed and added to ezCADD, available at http://dxulab.org/software .
尽管计算机辅助药物设计 (CADD) 软件可能看起来丰富且易于使用，但全球仍有大量的生物医学研究人员未得到充分服务，特别是那些没有计算培训和有限研究资金的研究人员。为了满足这一重要需求，并帮助科学家克服阻碍他们在药物发现工作中利用 CADD 的障碍，我们开发了 ezCADD，这是一种基于网络的 CADD 建模环境，体现了四个简单的设计理念：简单、快速、用户友好和 2D/3D 可视化。在本文中，我们描述了已在 ezCADD 中实现的三个基本应用程序的功能：小分子对接、蛋白质-蛋白质对接和结合口袋检测，以及它们在针对致病微生物酶的药物设计中的应用，作为一个示例。为了评估用户体验和我们实施的效果，我们将 ezCADD 引入到药物作用原理课程中，作为一年级药学学生的主动学习练习。该网络服务能够稳健地处理 95 个同时进行的分子对接作业。我们的调查数据显示，在 95 名参与的学生中，97%的学生在没有广泛培训的情况下，至少部分地独立完成了分子对接实验；88%的学生认为 ezCADD 简单易用；99-100%的学生认为 ezCADD 增强了对药物-受体结构和识别的理解；学生在分子建模和可视化方面的体验从零基础提高到了更高的水平。学生的反馈代表了非计算研究人员的用户体验基线数据。事实证明，除了支持药物发现研究外，ezCADD 还是促进科学、技术、工程和数学 (STEM) 教育的有效工具。更多先进的 CADD 应用程序正在开发中，并添加到 ezCADD 中，可在 http://dxulab.org/software 获得。
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