Computational chemistry

Modelling, simulation and analysis of biomolecular systems

Requirements

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

Material

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Analysis of molecular dynamics simulations
tutorial
High Throughput Molecular Dynamics and Analysis
tutorial
Protein-ligand docking
tutorial
Running molecular dynamics simulations using GROMACS
tutorial
Setting up molecular systems
tutorial
Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
tutorial

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.

Maintainers

This material is maintained by:

AvatarChristopher BarnettAvatarTharindu SenapathiAvatarSimon BrayAvatarBjörn 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:

Christopher BarnettTharindu SenapathiSimon BrayBjörn Grüning

References