T015 - Protein-ligand docking

devtools/conda-envs/test_env.yml

@@ -1,6 +1,7 @@
 name: teachopencadd
 channels:
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
   - python>=3.6
@@ -29,6 +30,7 @@ dependencies:
   - redo
   - requests-cache
   - suds-community
+  - smina
   ## CI tests
   # Workaround for https://github.com/computationalmodelling/nbval/issues/153
   - pytest 5.*

devtools/conda-envs/users_env.yml

@@ -4,6 +4,7 @@
 name: teachopencadd
 channels:
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
   - python>=3.6
@@ -32,6 +33,7 @@ dependencies:
   - redo
   - requests-cache
   - suds-community
+  - smina
   ## CI tests
   # Workaround for https://github.com/computationalmodelling/nbval/issues/153
   - pytest 5.*

docs/all_talktorials.rst

@@ -16,3 +16,4 @@ This is the complete list of talktorials available for online reading. Take into
    talktorials/T008_query_pdb.nblink
    talktorials/T009_compound_ensemble_pharmacophores.nblink
    talktorials/T010_binding_site_comparison.nblink
+   talktorials/T015_protein_ligand_docking.nblink

docs/talktorials/T015_protein_ligand_docking.nblink

@@ -0,0 +1 @@
+{"path": "../../teachopencadd/talktorials/T015_protein_ligand_docking/talktorial.ipynb", "extra-media": ["../../teachopencadd/talktorials/T015_protein_ligand_docking/images"]}

teachopencadd/talktorials/T015_protein_ligand_docking/README.md

@@ -1 +1,41 @@
-> This talktorial is still under development
+# T015 · Protein ligand docking
+
+Authors:
+
+- Jaime Rodríguez-Guerra, Volkamer lab, Charité
+- Dominique Sydow, Volkamer lab, Charité
+- Michele Wichmann, Volkamer lab, Charité
+- Maria Trofimova, CADD seminar, 2020, Charité/FU Berlin
+- David Schaller, Volkamer lab, Charité
+
+## Aim of this talktorial
+
+In this talktorial, we will use molecular docking to predict the binding mode of a small molecule in a protein binding site. The epidermal growth factor receptor (EGFR) will serve as a model system to explain important steps of a molecular docking workflow with the docking software Smina.
+
+### Contents in *Theory*
+
+- Molecular docking
+- Sampling algorithms
+- Scoring functions
+- Known limitations
+- Docking softwares
+  - Commercial
+  - Free (for academics)
+
+### Contents in *Practical*
+
+- Protein and ligand preparation
+- Binding site definition
+- Docking calculation
+- Docking results visualization
+
+### References
+- Pagadala et al. 2017 _Software for molecular docking: a review_ ([_Biophy Rev_ (2017), __9__, 91-102](https://doi.org/10.1007/s12551-016-0247-1))
+- Meng et al. 2011 _Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery_ ([_Curr Comput Aided Drug Des_ (2011), __7__, 2, 146-157](https://doi.org/10.2174/157340911795677602))
+- Gromski et al. 2019 _How to explore chemical space using algorithms and automation_ ([_Nat Rev Chem_ (2019), __3__, 119-128](https://doi.org/10.1038/s41570-018-0066-y))
+- Warren et al. 2006 _A critical assessment of docking programs and scoring functions_ ([_J Med Chem_ (2006), __49__, 20, 5912-31](https://doi.org/10.1021/jm050362n))
+- Wang et al. 2016 _Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power_ ([_Phys Chem Chem Phys_ (2016), __18__, 18, 12964-75](https://doi.org/10.1039/c6cp01555g))
+- Koes et al. 2013 _Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise_ ([_J Chem Inf Model_ (2013), __53__, 8, 1893-1904](https://doi.org/10.1021/ci300604z))
+- [OpenBabel](http://openbabel.org/wiki/Main_Page)
+- [Smina](https://sourceforge.net/projects/smina/)
+- [NGLView](http://nglviewer.org/nglview/latest/)