ArticlePLoS computational biology2014
Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed.
- Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.The Journal of chemical physics · 2021Article
- PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.Biophysicist (Rockville, Md.) · 2021Article
- Blending Gagne's Instructional Model with Peyton's Approach to Design an Introductory Bioinformatics Lesson Plan for Medical Students: Proof-of-Concept Study.JMIR medical education · 2018Article
- Extreme biophysics: Enzymes under pressure.Journal of computational chemistry · 2017Article
- ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.Journal of chemical information and modeling · 2015Article
- Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.Journal of chemical information and modeling · 2014Article
- Making biomolecular simulations accessible in the post-Nobel Prize era.PLoS computational biology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
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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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.