title: Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.
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.
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America.
authors: Benjamin T
authors: BT
authors: Miller
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America.
authors: Rishi P
authors: RP
authors: Singh
authors: Department of Natural Sciences, New College of Florida, Sarasota, Florida, United States of America.
authors: Vinushka
authors: V
authors: Schalk
authors: Department of Chemistry, University of South Florida, Tampa, Florida, United States of America.
authors: Yuri
authors: Y
authors: Pevzner
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America.
authors: Jingjun
authors: J
authors: Sun
authors: Department of Chemistry, Georgetown University, Washington, D.C., United States of America.
authors: Carrie S
authors: CS
authors: Miller
authors: Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
authors: Stefan
authors: S
authors: Boresch
authors: Department of Chemistry, Georgetown University, Washington, D.C., United States of America.
authors: Toshiko
authors: T
authors: Ichiye
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America.
authors: Bernard R
authors: BR
authors: Brooks
authors: Department of Chemistry, University of South Florida, Tampa, Florida, United States of America.
authors: H Lee
authors: HL
authors: Woodcock
mesh_terms: D019295:Computational Biology / Q000193:education*; D003198:Computer Simulation; D003194:Computer-Assisted Instruction / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D012984:Software