The increasing use of information technology in the discovery of new molecular entities encourages the use of modern molecular-modeling tools to help teach important concepts of drug design to chemistry and pharmacy undergraduate students. In particular, statistical models such as quantitative structure–activity relationships (QSAR)—often as its 3D QSAR variant—are commonly used in the development and optimization of a leading compound. We describe how these drug discovery methods can be taught and learned by means of free and open-source web applications, specifically the online platform www.3d-qsar.com. This new suite of web applications has been integrated into a drug design teaching course, one that provides both theoretical and practical perspectives. We include the teaching protocol by which pharmaceutical biotechnology master students at Pharmacy Faculty of Sapienza Rome University are introduced to drug design. Starting with a choice among recent articles describing the potencies of a series of molecules tested against a biological target, each student is expected to build a 3D QSAR ligand-based model from their chosen publication, proceeding as follows: creating the initial data set (Py-MolEdit); generating the global minimum conformations (Py-ConfSearch); proposing a promising mutual alignment (Py-Align); and finally, building, and optimizing a robust 3D QSAR models (Py-CoMFA). These student activities also help validate these new molecular modeling tools, especially for their usability by inexperienced hands. To more fully demonstrate the effectiveness of this protocol and its tools, we include the work performed by four of these students (four of the coauthors), detailing the satisfactory 3D QSAR models they obtained. Such scientifically complete experiences by undergraduates, made possible by the efficiency of the 3D QSAR methodology, provide exposure to computational tools in the same spirit as traditional laboratory exercises. With the obsolescence of the classic Comparative Molecular Field Analysis Sybyl host, the 3dqsar web portal offers one of the few available means of performing this well-established 3D QSAR method.

中文翻译：

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教学计算药物设计：通过Web应用程序对3D定量结构与活动关系的学生调查

信息技术在发现新的分子实体中的使用越来越广泛，这鼓励使用现代分子建模工具来帮助向化学和药学专业的本科生传授药物设计的重要概念。特别是，诸如定量结构-活性关系（QSAR）等统计模型（通常是其3D QSAR变体）通常用于开发和优化领先化合物。我们描述了如何通过免费和开源的Web应用程序，特别是在线平台www.3d-qsar.com来教授和学习这些药物发现方法。这套新的网络应用程序套件已集成到药物设计教学课程中，该课程提供了理论和实践的观点。我们包括了教学方案，通过该方案，萨皮恩扎罗马大学药学院的药物生物技术硕士生被介绍到药物设计中。从最近的文章中进行描述，这些文章描述了针对生物靶标测试的一系列分子的效力，每个学生都将从他们选择的出版物中构建基于3D QSAR配体的模型，过程如下：创建初始数据集（Py -MolEdit）; 生成全局最小构象（Py-ConfSearch）；提出有前途的相互一致（Py-Align）；最后，建立并优化强大的3D QSAR模型（​​Py-CoMFA）。这些学生活动还有助于验证这些新的分子建模工具，尤其是对于没有经验的人以确保其可用性。为了更充分地展示此协议及其工具的有效性，我们包括了其中四个学生（其中四个是合著者）所做的工作，详细介绍了他们获得的令人满意的3D QSAR模型。3D QSAR方法的高效性使大学生获得了如此科学的完整体验，使他们可以像传统实验室练习一样接触计算工具。随着经典比较分子场分析Sybyl宿主的淘汰，3dqsar网站门户提供了执行这种公认的3D QSAR方法的少数可用方法之一。以与传统实验室练习相同的精神提供对计算工具的了解。随着经典比较分子场分析Sybyl宿主的淘汰，3dqsar网站门户提供了执行这种公认的3D QSAR方法的少数可用方法之一。以与传统实验室练习相同的精神提供对计算工具的了解。随着经典比较分子场分析Sybyl宿主的淘汰，3dqsar网站门户提供了执行这种公认的3D QSAR方法的少数可用方法之一。