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Design and Implementation of an Accessible and Open-Sourced "In Silico" Drug Screening Activity for Cancer Drug Discovery
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Audrey G. Fikes; Melissa C. Srougi – Journal of Chemical Education, 2023
The application of chemistry concepts in biological settings plays an important role in the interdisciplinary field of drug discovery and development. This is true for molecular docking, where an understanding of intermolecular forces and noncovalent interactions is useful for rational drug design and development. Here we report the design and use…
Descriptors: Chemistry, Science Instruction, Molecular Structure, Drug Therapy
Computer-Assisted Conformational Analysis of Small Molecules Using VEGA ZZ, a Freely Available Software Program, as an Introduction to Molecular Modeling
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Soule`re, Laurent – Journal of Chemical Education, 2021
We report a molecular modeling study for undergraduate students aimed at carrying out an analysis of small molecules using a systematic conformational search with VEGA ZZ, a freely available software program. Conformational analyses were performed using a systematic search based on variations of torsion angles. First, the conformations of n-butane…
Descriptors: Computer Assisted Instruction, Computer Software, Open Source Technology, Undergraduate Students
Teaching and Learning Computational Drug Design: Student Investigations of 3D Quantitative Structure--Activity Relationships through Web Applications
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Ragno, Rino; Esposito, Valeria; Di Mario, Martina; Masiello, Stefano; Viscovo, Marco; Cramer, Richard D. – Journal of Chemical Education, 2020
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…
Descriptors: Chemistry, Computer Uses in Education, Pharmaceutical Education, Graduate Students
Molecular Docking with Open Access Software: Development of an Online Laboratory Handbook and Remote Workflow for Chemistry and Pharmacy Master's Students to Undertake Computer-Aided Drug Design
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Clent, Bethanie A.; Wang, Yuhang; Britton, Hugh C.; Otto, Frank; Swain, Christopher J.; Todd, Matthew H.; Wilden, Jonathan D.; Tabor, Alethea B. – Journal of Chemical Education, 2021
In response to the closure of many university laboratories due to the COVID-19 pandemic in 2020, a handbook and remote webinar approach designed to support students in the use of software tools for computer-aided drug design has been developed. Specifically, the course has been designed for chemistry and pharmacy students who have little or no…
Descriptors: Science Laboratories, Pharmacology, Drug Therapy, School Closing
Development and Use of an Open-Source, User-Friendly Package to Simulate Voltammetry Experiments
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Wang, Shuo; Wang, Jing; Gao, Yanjing – Journal of Chemical Education, 2017
An open-source electrochemistry simulation package has been developed that simulates the electrode processes of four reaction mechanisms and two typical electroanalysis techniques: cyclic voltammetry and chronoamperometry. Unlike other open-source simulation software, this package balances the features with ease of learning and implementation and…
Descriptors: Open Source Technology, Computer Simulation, Chemistry, Graduate Students
Molecular Dynamics Characterization of the Conformational Landscape of Small Peptides: A Series of Hands-On Collaborative Practical Sessions for Undergraduate Students
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Rodrigues, João P. G. L. M.; Melquiond, Adrien S. J.; Bonvin, Alexandre M. J. J. – Biochemistry and Molecular Biology Education, 2016
Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These…
Descriptors: Molecular Structure, Hands on Science, Undergraduate Students, Open Source Technology