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
Analysis of molecular dynamics simulations
Intermediate
tutorial
High Throughput Molecular Dynamics and Analysis
Advanced
tutorial
Protein-ligand docking
Intermediate
tutorial
Running molecular dynamics simulations using GROMACS
Intermediate
tutorial
Setting up molecular systems
Intermediate
tutorial
Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring
Intermediate
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 Barnett AvatarTharindu Senapathi AvatarSimon Bray AvatarBjörn 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:

AvatarChristopher Barnett AvatarTharindu Senapathi AvatarSimon Bray AvatarBjörn Grüning

References