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
Analysis of molecular dynamics simulations
Data management in Medicinal Chemistry
High Throughput Molecular Dynamics and Analysis
Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
Protein-ligand docking
Running molecular dynamics simulations using GROMACS
Setting up molecular systems
Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring

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.

Editorial Board

This material is reviewed by our Editorial Board:

Christopher Barnett avatar Christopher BarnettTharindu Senapathi avatar Tharindu SenapathiSimon Bray avatar Simon Brayorcid logoBjörn Grüning avatar 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:

Tharindu Senapathi avatar Tharindu SenapathiSimon Bray avatar Simon BrayChristopher Barnett avatar Christopher Barnettorcid logoBjörn Grüning avatar Björn GrüningJulia Jakiela avatar Julia Jakielaorcid logoNadia Goué avatar Nadia Gouéorcid logoAurélien F. A. Moumbock avatar Aurélien F. A. Moumbock

Funders

This material was funded by:

ELIXIR-UK: FAIR Data Stewardship training avatar ELIXIR Fair Data

References