From cd59303581169420486dc0112814f19707831339 Mon Sep 17 00:00:00 2001 From: Unknown Date: Thu, 14 Oct 2021 14:44:09 +0200 Subject: [PATCH 1/4] README: Update external resources --- README.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 1c48a219..8f372e6c 100644 --- a/README.md +++ b/README.md @@ -155,7 +155,7 @@ It will help measure the impact of the TeachOpenCADD platform and future funding - Cheminformatics and structural bioinformatics: [`rdkit`](http://rdkit.org/), - [`openbabel`](http://openbabel.org/wiki/), + [`openbabel`](https://openbabel.org/), [`mdanalysis`](https://www.mdanalysis.org/), [`biopython`](https://biopython.org/), [`biopandas`](http://rasbt.github.io/biopandas/), @@ -166,12 +166,13 @@ It will help measure the impact of the TeachOpenCADD platform and future funding [`openmmforcefields`](https://github.com/openmm/openmmforcefields), [`pdbfixer`](https://github.com/openmm/pdbfixer), [`mdanalysis`](https://www.mdanalysis.org/), - [`biotite`](https://www.biotite-python.org/) + [`biotite`](https://www.biotite-python.org/), + [`smina`](https://sourceforge.net/p/smina/discussion/) - Data science (PyData stack): [`numpy`](https://numpy.org/), [`pandas`](https://pandas.pydata.org/), [`scikit-learn`](https://scikit-learn.org/), - [`tensorflow`](https://www.tensorflow.org/), + [`keras`](https://keras.io/), [`jupyter`](https://jupyter.org/), [`ipywidgets`](https://ipywidgets.readthedocs.io) - Data visualization: @@ -201,12 +202,15 @@ It will help measure the impact of the TeachOpenCADD platform and future funding - Code style: [`black-nb`](https://github.com/tomcatling/black-nb) -#### Databases +#### Databases and webservers - [ChEMBL](https://www.ebi.ac.uk/chembl/) - [RCSB PDB](https://www.rcsb.org/) - [KLIFS](https://klifs.net/) - [PubMed](https://pubchem.ncbi.nlm.nih.gov/) +- [ProteinsPlus](https://proteins.plus/) + +If we are using your resource and forgot to add it here, please contact us so that we can rectify this, thank you! ### Funding From 4875821e45c8b72857593bbe4321887c1741e6f0 Mon Sep 17 00:00:00 2001 From: Unknown Date: Thu, 14 Oct 2021 14:44:22 +0200 Subject: [PATCH 2/4] Docs: Add ref to TOC book chapter --- docs/index.rst | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/docs/index.rst b/docs/index.rst index f590eb46..3f79b20f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -61,6 +61,7 @@ If you make use of the TeachOpenCADD material in scientific publications, please - `TeachOpenCADD Jupyter Notebooks: Talktorials T001-T010 `_ - `TeachOpenCADD KNIME workflows `_ +- `How to use the TeachOpenCADD material for teaching? `_ It will help measure the impact of the TeachOpenCADD platform and future funding! @@ -90,6 +91,16 @@ It will help measure the impact of the TeachOpenCADD platform and future funding year = {2019} } + @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}, + } + Funding ------- @@ -97,6 +108,7 @@ Funding Volkamer Lab's projects are supported by several public funding sources (for more info see our `webpage `_). + License ------- From 8648d338d34d4c28052431b541862610bc363df3 Mon Sep 17 00:00:00 2001 From: Unknown Date: Thu, 14 Oct 2021 14:44:36 +0200 Subject: [PATCH 3/4] Docs: Add link to external resources used in TOC --- docs/external_resources.rst | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/external_resources.rst b/docs/external_resources.rst index f6856d4e..864172c7 100644 --- a/docs/external_resources.rst +++ b/docs/external_resources.rst @@ -18,4 +18,10 @@ The following resources are collections of interesting cheminformatics-related t - `Curated list of resources from the RDKit UGM 2020 `_ - `A Highly Opinionated List of Open Source Cheminformatics Resources `_ by Pat Walters -- `Awesome Cheminformatics `_ by Yi Hsiao \ No newline at end of file +- `Awesome Cheminformatics `_ by Yi Hsiao + + +Packages and webservers used in TeachOpenCADD +--------------------------------------------- + +Please find the full list on `GitHub `_. \ No newline at end of file From 2c396bf2c30a8a16379b3743328ea8ad7d3f1ae7 Mon Sep 17 00:00:00 2001 From: Unknown Date: Thu, 14 Oct 2021 14:47:32 +0200 Subject: [PATCH 4/4] README: Cross-reference external resources used in TOC --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8f372e6c..889e2470 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ Open source programming packages for cheminformatics and structural bioinformati 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. -For each topic, an interactive Jupyter Notebook is offered, using open source packages such as the Python packages `rdkit`, `pypdb`, `biopandas`, `nglview`, and `mdanalysis`. 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. +For each topic, an interactive Jupyter Notebook is offered, using open source packages such as the Python packages `rdkit`, `pypdb`, `biopandas`, `nglview`, and `mdanalysis` (find the full list [here](https://github.com/volkamerlab/teachopencadd#external-resources)). 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. > If you use TeachOpenCADD in a publication, > please [cite](https://github.com/volkamerlab/TeachOpenCADD/blob/master/README.md#citation) us!