A Computer-Aided Drug Discovery System for Chemistry Teaching

Gledhill, Robert J.; Kent, Sarah; Hudson, Brian D.; Richards, William G.; Essex, Jonathan W.; Frey, Jeremy G.

doi:10.1021/ci050383q

Cited by 10 publications

(10 citation statements)

References 15 publications

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“…Finally, ViPA was originally implemented as command‐line software, and as has been recently pointed out, researchers often do not like using command‐line‐driven software, even if performing the same task another way requires a great deal more time 50, 51. Increasingly, scientific software is being designed with web‐based interfaces, making access simpler and more familiar and, therefore, making the software more likely to be used 52–66…”

Section: Introductionmentioning

confidence: 99%

Vibalizer: A free, web‐based tool for rapid, quantitative comparison and analysis of calculated vibrational modes

Grafton¹

2007

J Comput Chem

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This report describes the development and applications of a software package called Vibalizer, the first and only method that provides free, fast, interactive, and quantitative comparison and analysis of calculated vibrational modes. Using simple forms and menus in a web-based interface, Vibalizer permits the comparison of vibrational modes from different, but similar molecules and also performs rapid calculation and comparison of isotopically substituted molecules' normal modes. Comparing and matching complex vibrational modes can be completed in seconds with Vibalizer, whereas matching vibrational modes manually can take hours and gives only qualitative comparisons subject to human error and differing individual judgments. In addition to these core features, Vibalizer also provides several other useful features, including the ability to automatically determine first-approximation mode descriptions, to help users analyze the results of vibrational frequency calculations. Because the software can be dimensioned to handle almost arbitrarily large systems, Vibalizer may be of particular use when analyzing the vibrational modes of complex systems such as proteins and extended materials systems. Additionally, the ease of use of the Vibalizer interface and the straightforward interpretation of results may find favor with educators who incorporate molecular modeling into their classrooms. The Vibalizer interface is available for free use at http://www. compchem.org, and it is also available as a locally-installable package that will run on a Linux-based web server.

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Section: Introductionmentioning

confidence: 99%

Vibalizer: A free, web‐based tool for rapid, quantitative comparison and analysis of calculated vibrational modes

Grafton¹

2007

J Comput Chem

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“…Not surprisingly, the above-mentioned courses and sessions are merely dedicated to upper-level undergraduate students. A noticeable exception is the e-malaria project, which was used to introduce high-school students to drug design in a real-life context . Unfortunately, this latter endeavor faced licensing and confidentiality issues that required a complex hardware and network infrastructure along with an account login procedure.…”

Section: Pedagogical Objectivesmentioning

confidence: 99%

“…A noticeable exception is the e-malaria project, which was used to introduce high-school students to drug design in a real-life context. 35 Unfortunately, this latter endeavor faced licensing and confidentiality issues that required a complex hardware and network infrastructure along with an account login procedure. Together with significant computational time, this lack of flexibility hinders the trial-and-error cyclic process, which we consider key to appreciating the basis of molecular design.…”

Section: ■ Introductionmentioning

confidence: 99%

Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public

et al. 2017

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Due to its impact on society, the design of new drugs has the potential to interest a wide audience, and provides a rare opportunity to introduce several concepts in chemistry and biochemistry. Drug design can be seen as a multiobjective cyclic optimization process. Indeed, it is important to develop the understanding not only that a drug is generally an effective ligand for a protein of therapeutic interest, but also that these molecules need to have drug-like properties. Computer-aided drug design and bioinformatics approaches play a fundamental role in addressing these different challenges. Here we introduce a new freely available integrated web-based educational tool, Drug Design Workshop, which presents the basics of drug design and provides anyone with access to computational methods and resources to conceive and evaluate molecules for their potential to become actual drugs. We provide 3 examples of drug design targets for the discovery of common or state-of-the-art drugs, which can be used by educators to introduce easily the different concepts related to drug discovery: anti-inflammatory agents and drugs for immunotherapy or targeted cancer therapy. Since 2015, the workshop has been successfully given to over 1,500 people. The Web site was optimized on the basis of the positive and constructive comments from high-school teachers and students (15–19 years old).

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“…In Section 2 we highlight the security issues that were a major concern to us and in Section 3 we summarize the creation of the initial schools e-Malaria system, describing the development and refinement of the system architecture, the user interface and administrative systems (additional details are available in the chemistry literature [17]), and discuss the docking Grid in greater detail in Section 4. In Section 5, we discuss the lessons learnt from the initial testing and evaluation of the system, and the resulting design of the interface to the Web site is discussed in Section 6.…”

Section: Introductionmentioning

confidence: 99%

e‐Malaria: the schools Malaria project

Geldhill

Kent

Milsted

et al. 2007

Concurrency and Computation

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SUMMARYe-Malaria (http://emalaria.soton.ac.uk/) aims to bring together 16-18 year old school students with university researchers to explain aspects of computational drug design using the example of the hunt for a new anti-Malaria drug. Malaria kills a child every 30 seconds, and 40% of the world's population lives in countries where the disease is endemic. Resistance to existing drugs is increasing and there is a growing need for new compounds. This challenge is being offered to school students who will use a distributed drug search and selection system via a Web interface to design potential drugs. The project makes use of industrial code for the docking study ('GOLD') and as such presents valuable lessons in how to achieve the integration of industrial programs into a 'free' outreach environment. The results of the trials are displayed in an accessible manner, giving students an opportunity for discussion and debate both with peers and with university contacts. The initial project has been extended to provide a similar challenge for undergraduate chemists as part of a chemical informatics course at a level relevant to more advances chemical skills.

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A Computer-Aided Drug Discovery System for Chemistry Teaching

Cited by 10 publications

References 15 publications

Vibalizer: A free, web‐based tool for rapid, quantitative comparison and analysis of calculated vibrational modes

Vibalizer: A free, web‐based tool for rapid, quantitative comparison and analysis of calculated vibrational modes

Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public

e‐Malaria: the schools Malaria project

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