Merge pull request #155 from volkamerlab/update-readme-docs

Update README and docs

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!
@@ -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
 

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 <https://github.com/rdkit/UGM_2020/blob/master/info/curated_list_of_resources.md>`_
 - `A Highly Opinionated List of Open Source Cheminformatics Resources <https://github.com/PatWalters/resources/blob/main/cheminformatics_resources.md>`_ by Pat Walters
-- `Awesome Cheminformatics <https://github.com/hsiaoyi0504/awesome-cheminformatics#resources>`_ by Yi Hsiao
+- `Awesome Cheminformatics <https://github.com/hsiaoyi0504/awesome-cheminformatics#resources>`_ by Yi Hsiao
+
+
+Packages and webservers used in TeachOpenCADD
+---------------------------------------------
+
+Please find the full list on `GitHub <https://github.com/volkamerlab/teachopencadd#external-resources>`_.

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 <https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0351-x>`_
 - `TeachOpenCADD KNIME workflows <https://pubs.acs.org/doi/10.1021/acs.jcim.9b00662>`_
+- `How to use the TeachOpenCADD material for teaching? <https://pubs.acs.org/doi/abs/10.1021/bk-2021-1387.ch010>`_
 
 It will help measure the impact of the TeachOpenCADD platform and future funding!
 
@@ -90,13 +91,24 @@ 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
 -------
 
 Volkamer Lab's projects are supported by several public funding sources
 (for more info see our `webpage <https://volkamerlab.org/>`_).
 
+
 License
 -------