Modelling, simulation and analysis of biomolecular systemsYou can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.
Before diving into this topic, we recommend you to have a look at:
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -p 8080:80 quay.io/galaxy/computational-chemistry-training
NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.
Frequently Asked QuestionsCommon questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.
This material is maintained by:Christopher BarnettTharindu SenapathiSimon BrayBjörn Grüning
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
This material was contributed to by:Nadia GouéAurélien F. A. MoumbockBjörn GrüningChristopher BarnettTharindu SenapathiSimon Bray
galaxycomputationalchemistry: The Galaxy Computational Chemistry group
source repositories for computational chemistry tools
Senapathi et al.: Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
scientificomputing: Overview of the bridge platform
Overview of the bridge platform
Jo et al.: CHARMM-GUI 10 years for biomolecular modeling and simulation.
Naidoo et al.: Molecular Details from Computational Reaction Dynamics for the Cellobiohydrolase I Glycosylation Reaction
7CEL simulation reaction mechanism reference
Abraham et al.: GROMACS - High performance molecular simulations through multi-level parallelism from laptops to supercomputers