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TeachOpenCADD
A teaching platform for computer-aided drug design (CADD) using open source packages and data.
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Description
<p align="center"> <img src="docs/_static/images/TeachOpenCADD_topics.png" alt="TeachOpenCADD topics" width="800"/> <br> <font size="1"> Figure adapted from Figure 1 in the TeachOpenCADD publication <a href="https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0351-x"> (D. Sydow <i>et al.</i>, J. Cheminformatics, 2019)</a>. </font> </p>Open source programming packages for cheminformatics and structural bioinformatics are powerful tools to build modular, reproducible, and reusable pipelines for computer-aided drug design (CADD). While documentation for such tools is available, only few freely accessible examples teach underlying concepts focused on CADD applications, addressing especially users new to the field.
TeachOpenCADD is a teaching platform developed by students for students, which provides teaching material for central CADD topics. Since we cover both the theoretical as well as practical aspect of these topics, the platform addresses students and researchers with a biological/chemical as well as a computational background.
Each topic is covered in an interactive Jupyter Notebook, using open source packages such as the Python packages rdkit, pypdb, biopandas, nglview, and mdanalysis (find the full list here). Topics are continuously expanded and open for contributions from the community. Beyond their teaching purpose, the TeachOpenCADD material can serve as starting point for users’ project-directed modifications and extensions.
New edition: we have extended the TeachOpenCADD platform with 6 notebooks introducing deep learning and its application to CADD related topics.
Get started
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If you can't wait and just want to read through the materials, please go to the read-only version here.
If you'd like to execute the provided notebooks, we offer two possibilities:
<!-- markdown-link-check-disable-next-line -->- Online thanks to Binder. This takes around 10 minutes to get ready, but does not require any kind of setup on your end. Click here to get started: . Once it has loaded, you can navigate to
teachopencadd/talktorials/to find the executable notebooks. - Locally using our
condapackage. More details in this section of the documentation.
TeachOpenCADD KNIME workflows
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If you prefer to work in the context of a graphical interface, talktorials T001-T008 are also available as KNIME workflows. Questions regarding this version should be addressed using the "Discussion section" available at this post. You need to create a KNIME account to use the forum.
About TeachOpenCADD
External resources
Please refer to our TeachOpenCADD website to find a list of external resources:
- External packages and webservices that are used in the TeachOpenCADD material
- Further reading material on Python programming, cheminformatics, structural bioinformatics, and more.