Titel
Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial
Autor*in
Benjamin T. Miller
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, United States of America
Autor*in
Rishi P. Singh
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, United States of America
Autor*in
Vinushka Schalk
Department of Natural Sciences, New College of Florida
... show all
Abstract
This article describes the development, implementation, and use of web-based “lessons” to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that “point and click” simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.
Stichwort
Simulation and modelingBiophysical simulationsWeb-based applicationsBiochemical simulationsSolvationComputer softwareUser interfacesProtein structure
Objekt-Typ
Sprache
Englisch [eng]
Persistent identifier
https://phaidra.univie.ac.at/o:467424
Erschienen in
Titel
PLoS Computational Biology
Band
10
Ausgabe
7
Verlag
Public Library of Science (PLoS)
Erscheinungsdatum
2014
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