ezCADD: A Rapid 2D/3D Visualization-Enabled Web ModelingEnvironment for Democratizing Computer-Aided Drug Design

摘要

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 showedthat among the 95 participating students, 97% completed the moleculardocking experiment on their own at least partially without extensivetraining; 88% considered ezCADD easy and user-friendly; 99–100%agreed that ezCADD enhanced the understanding of drug–receptorstructures and recognition; and the student experience in molecularmodeling and visualization was significantly improved from zero toa higher level. The student feedback represents the baseline dataof user experience from noncomputational researchers. It is demonstratedthat in addition to supporting drug discovery research, ezCADD isalso an effective tool for promoting science, technology, engineering,and mathematics (STEM) education. More advanced CADD applicationsare being developed and added to ezCADD, available at .