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Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

Miller BT, Singh RP, Schalk V, Pevzner Y, Sun J, Miller CS, Boresch S, Ichiye T, Brooks BR, Woodcock HL - PLoS Comput. Biol. (2014)

Bottom Line: This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules.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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America.

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.

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Examples of using GLmol for visualization.(A) Ubiquitin (PDB code 1UBQ [57]) displayed as ribbons with crystal waters. (B) A ball-and-stick representation of a small peptide (PDB code 1YJP [27]).
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pcbi-1003719-g003: Examples of using GLmol for visualization.(A) Ubiquitin (PDB code 1UBQ [57]) displayed as ribbons with crystal waters. (B) A ball-and-stick representation of a small peptide (PDB code 1YJP [27]).

Mentions: Although JSmol is extremely functional with wide-ranging compatibility, its graphical performance lags behind best-in-class desktop applications [53],[54]. Therefore, we also integrated GLmol into CHARMMing. GLmol is a 3-D molecular viewer based on modern web graphics; i.e., WebGL (Web Graphics Library). The WebGL-based GLmol offers advanced Graphics Processing Unit (GPU) accelerated visualization of 3-D molecular structures. In fact, performance and image quality (Figure 3) of GLmol can rival desktop applications; e.g., VMD [53], PyMol [54]. Although the quality and performance of GLmol is outstanding, JSmol offers far more functionality; therefore, we have chosen to use the latter to implement more recent CHARMMing features that require the end user to interact with a display. However, both GLmol and JSmol may be used for visualization.


Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

Miller BT, Singh RP, Schalk V, Pevzner Y, Sun J, Miller CS, Boresch S, Ichiye T, Brooks BR, Woodcock HL - PLoS Comput. Biol. (2014)

Examples of using GLmol for visualization.(A) Ubiquitin (PDB code 1UBQ [57]) displayed as ribbons with crystal waters. (B) A ball-and-stick representation of a small peptide (PDB code 1YJP [27]).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109840&req=5

pcbi-1003719-g003: Examples of using GLmol for visualization.(A) Ubiquitin (PDB code 1UBQ [57]) displayed as ribbons with crystal waters. (B) A ball-and-stick representation of a small peptide (PDB code 1YJP [27]).
Mentions: Although JSmol is extremely functional with wide-ranging compatibility, its graphical performance lags behind best-in-class desktop applications [53],[54]. Therefore, we also integrated GLmol into CHARMMing. GLmol is a 3-D molecular viewer based on modern web graphics; i.e., WebGL (Web Graphics Library). The WebGL-based GLmol offers advanced Graphics Processing Unit (GPU) accelerated visualization of 3-D molecular structures. In fact, performance and image quality (Figure 3) of GLmol can rival desktop applications; e.g., VMD [53], PyMol [54]. Although the quality and performance of GLmol is outstanding, JSmol offers far more functionality; therefore, we have chosen to use the latter to implement more recent CHARMMing features that require the end user to interact with a display. However, both GLmol and JSmol may be used for visualization.

Bottom Line: This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules.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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America.

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.

Show MeSH