Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial
نویسندگان
چکیده
منابع مشابه
Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial
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 inte...
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A module for fast determination of reduction potentials, E°, of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org). The free energy of reduction, which is proportional to E°, is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic c...
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A lesson utilizing a coarse-grained (CG) Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool ...
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DEVS-based modeling and simulation have been applied to many different fields and used by researchers from all over the world. Much progress has been made in developing DEVS-based modeling and simulation environments. However, less work exists in developing systems that help beginners to learn DEVS models and DEVS-based simulation. This paper presents an interactive web-based tutorial system fo...
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ژورنال
عنوان ژورنال: PLoS Computational Biology
سال: 2014
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1003719