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61 changes: 46 additions & 15 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -109,49 +109,80 @@ To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0

## Citation

If you make use of the TeachOpenCADD material in scientific publications, please cite our respective articles:
If you make use of the TeachOpenCADD material in scientific publications, please cite our respective articles. It will help measure the impact of the TeachOpenCADD platform and future funding, thank you!

- [TeachOpenCADD Jupyter Notebooks: Talktorials T001-T010](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0351-x)
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- [TeachOpenCADD KNIME workflows](https://pubs.acs.org/doi/10.1021/acs.jcim.9b00662)
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- [How to use the TeachOpenCADD material for teaching?](https://pubs.acs.org/doi/abs/10.1021/bk-2021-1387.ch010)
### TeachOpenCADD Jupyter notebooks

TeachOpenCADD Jupyter notebooks' main citation: Talktorials T001-T022 ([paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac267/6582172))

```
@article{TeachOpenCADD2022,
author = {Sydow, Dominique and Rodríguez-Guerra, Jaime and Kimber, Talia B and Schaller, David and Taylor, Corey J and Chen, Yonghui and Leja, Mareike and Misra, Sakshi and Wichmann, Michele and Ariamajd, Armin and Volkamer, Andrea},
title = {TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research},
journal = {Nucleic Acids Research},
year = {2022},
doi = {10.1093/nar/gkac267},
}
```

It will help measure the impact of the TeachOpenCADD platform and future funding!
TeachOpenCADD Jupyter notebooks' original citation: Talktorials T001-T010 ([paper](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0351-x))

```
@article{TeachOpenCADD2019,
author = {Sydow, Dominique and Morger, Andrea and Driller, Maximilian and Volkamer, Andrea},
title = {{TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data}},
doi = {10.1186/s13321-019-0351-x},
url = {https://doi.org/10.1186/s13321-019-0351-x},
journal = {J. Cheminform.},
journal = {Journal of Cheminformatics},
year = {2019},
volume = {11},
number = {1},
pages = {29},
year = {2019}
doi = {10.1186/s13321-019-0351-x},
}
```

<!-- markdown-link-check-disable-next-line -->
TeachOpenCADD Jupyter notebooks on kinase similarities: Talktorials T023-T028 ([paper](https://doi.org/10.33011/livecoms.3.1.1599))

```
@article{TeachOpenCADDKinaseEdition,
author = {Kimber, Talia B and Sydow, Dominique and Volkamer, Andrea},
title = {{Kinase similarity assessment pipeline for off-target prediction [v1.0]}},
journal = {Living Journal of Computational Molecular Science},
year = {2022},
doi = {10.1186/s13321-019-0351-x},
}
```

### TeachOpenCADD-KNIME

<!-- markdown-link-check-disable-next-line -->
TeachOpenCADD KNIME workflows ([paper](https://pubs.acs.org/doi/10.1021/acs.jcim.9b00662))

```
@article{TeachOpenCADDKNIME2019,
author = {Sydow, Dominique and Wichmann, Michele and Rodríguez-Guerra, Jaime and Goldmann, Daria and Landrum, Gregory and Volkamer, Andrea},
title = {{TeachOpenCADD-KNIME: A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows}},
doi = {10.1021/acs.jcim.9b00662},
url = {https://doi.org/10.1021/acs.jcim.9b00662},
journal = {Journal of Chemical Information and Modeling},
year = {2019},
volume = {59},
number = {10},
pages = {4083-4086},
year = {2019}
doi = {10.1021/acs.jcim.9b00662},
}
```

### Teaching
<!-- markdown-link-check-disable-next-line -->
How to use the TeachOpenCADD material for teaching ([chapter](https://pubs.acs.org/doi/abs/10.1021/bk-2021-1387.ch010))

```
@inbook{doi:10.1021/bk-2021-1387.ch010,
author = {Sydow, Dominique and Rodríguez-Guerra, Jaime and Volkamer, Andrea},
title = {Teaching Computer-Aided Drug Design Using TeachOpenCADD},
booktitle = {Teaching Programming across the Chemistry Curriculum},
chapter = {10},
pages = {135-158},
doi = {10.1021/bk-2021-1387.ch010},
URL = {https://pubs.acs.org/doi/abs/10.1021/bk-2021-1387.ch010},
}
```

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