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
level level level
tutorial zenodo_link workflow
High Throughput Molecular Dynamics and Analysis
level level level
tutorial zenodo_link workflow
Protein-ligand docking
level level level
tutorial workflow
Running molecular dynamics simulations using GROMACS
level level level
tutorial zenodo_link workflow
Setting up molecular systems
level level level
tutorial zenodo_link
Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring
level level level
tutorial zenodo_link workflow

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 admin to access everything.

Maintainers

This material is maintained by:

Christopher BarnettChristopher Barnett, Tharindu SenapathiTharindu Senapathi, Simon BraySimon Bray, Björn GrüningBjörn 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 BarnettChristopher Barnett, Tharindu SenapathiTharindu Senapathi, Simon BraySimon Bray, Björn GrüningBjörn Grüning

References