Computational chemistry

Modelling, simulation and analysis of biomolecular systems

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses

Material

Galaxy instances

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 Questions

Common 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.

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Editorial Board

This material is reviewed by our Editorial Board:

Christopher Barnett

Tharindu Senapathi

Simon Bray

Björn Grüning

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Nadia Goué

Tharindu Senapathi

Björn Grüning

Katarzyna Kamieniecka

Christopher Barnett

Simon Bray

Julia Jakiela

Aurélien F. A. Moumbock

Krzysztof Poterlowicz

Funders

This material was funded by:

DASH UK

References

• galaxycomputationalchemistry: The Galaxy Computational Chemistry group
  source repositories for computational chemistry tools
• Senapathi et al.: Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
  BRIDGE publication
• scientificomputing: Overview of the bridge platform
  Overview of the bridge platform
• Jo et al.: CHARMM-GUI 10 years for biomolecular modeling and simulation.
  CHARMM-GUI reference
• 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
  GROMACS reference