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Journal of chemical information and modeling
01 28, 2019;59 (1): 18-24.

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

Aoxiang Tao, Yuying Huang, Yasuhiro Shinohara, Matthew L Caylor, Srinath Pashikanti, Dong Xu
Author Information
  1. Aoxiang Tao: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kasiska Division of Health Sciences , Idaho State University , Meridian , Idaho 83642 , United States. ORCID
  2. Yuying Huang: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kasiska Division of Health Sciences , Idaho State University , Meridian , Idaho 83642 , United States.
  3. Yasuhiro Shinohara: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kasiska Division of Health Sciences , Idaho State University , Meridian , Idaho 83642 , United States.
  4. Matthew L Caylor: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kasiska Division of Health Sciences , Idaho State University , Meridian , Idaho 83642 , United States.
  5. Srinath Pashikanti: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kasiska Division of Health Sciences , Idaho State University , Meridian , Idaho 83642 , United States.
  6. Dong Xu: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kasiska Division of Health Sciences , Idaho State University , Meridian , Idaho 83642 , United States. ORCID
PMID: 30403855 DOI: 10.1021/acs.jcim.8b00633

Abstract

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 .

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Grants

  1. P20 GM103408/NIGMS NIH HHS
  2. P20 GM109095/NIGMS NIH HHS
  3. U54 GM104944/NIGMS NIH HHS

MeSH Term

Computer-Aided Design
Drug Design
Humans
Imaging, Three-Dimensional
Molecular Docking Simulation
Software
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't
Article has an altmetric score of 17

Word Cloud

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