e-learning
Setting up molecular systems
Abstract
In this tutorial, we'll cover the basics of molecular modelling by setting up a protein in complex with a ligand and uploading the structure to Galaxy. This tutorial will make use of CHARMM-GUI. Please note that the follow-up to this tutorial (located in Running molecular dynamics simulations using NAMD) requires access to NAMD Galaxy tools, which can be accessed using the Docker container but are currently not available on any public Galaxy server.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How to get started modelling a protein and a ligand?
Learning Objectives
- learn about the Protein Data Bank
- learn how to set up up a model protein and ligand system (with CHARMM-GUI)
- learn how to upload the system to Galaxy
Licence: Creative Commons Attribution 4.0 International
Keywords: Computational chemistry
Competency level: •• Intermediate
Target audience: Students
Resource type: e-learning
Version: 14
Status: Active
Prerequisites:
- Introduction to Galaxy Analyses
- Setting up molecular systems
Learning objectives:
- learn about the Protein Data Bank
- learn how to set up up a model protein and ligand system (with CHARMM-GUI)
- learn how to upload the system to Galaxy
Date modified: 2023-11-09
Date published: 2019-06-03
Authors: Christopher Barnett, Simon Bray, 
Nadia Goué
Contributors: Christopher Barnett, Gildas Le Corguillé, Simon Bray, Björn Grüning, Bérénice Batut, Helena Rasche, Saskia Hiltemann
Scientific topics: Computational chemistry
Activity log
