Computational chemistry

Modelling, simulation and analysis of biomolecular systems

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Requirements

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

Material

Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
Analysis of molecular dynamics simulations
tutorial
High Throughput Molecular Dynamics and Analysis
tutorial
  • Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
    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 Brayorcid logoAvatarBjörn 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 BarnettAvatarTharindu SenapathiAvatarSimon Brayorcid logoAvatarNadia Gouéorcid logoAvatarBjörn Grüningorcid logoAvatarAurélien F. A. Moumbock

    References