Merge pull request #82 from volkamerlab/das-015-revamp

T015 - Protein-ligand docking
volkamerlab · Feb 2, 2021 · 4ce7ba6 · 4ce7ba6
2 parents 2ecfe72 + 3476482
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diff --git a/devtools/conda-envs/test_env.yml b/devtools/conda-envs/test_env.yml
@@ -29,6 +29,7 @@ dependencies:
   - redo
   - requests-cache
   - suds-community
+  - smina
   ## CI tests
   # Workaround for https://github.com/computationalmodelling/nbval/issues/153
   - pytest 5.*

diff --git a/devtools/conda-envs/users_env.yml b/devtools/conda-envs/users_env.yml
@@ -32,6 +32,7 @@ dependencies:
   - redo
   - requests-cache
   - suds-community
+  - smina
   ## CI tests
   # Workaround for https://github.com/computationalmodelling/nbval/issues/153
   - pytest 5.*

diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
@@ -39,6 +39,10 @@ requirements:
     - mdanalysis
     - plip
     - biopython<=1.77
+    - redo
+    - requests-cache
+    - suds-community
+    - smina
     # note there are some pip dependencies not available in conda yet!
     # check /environment.yml for details
 

diff --git a/docs/all_talktorials.rst b/docs/all_talktorials.rst
@@ -18,4 +18,5 @@ This is the complete list of talktorials available for online reading. Take into
    talktorials/T010_binding_site_comparison.nblink
    talktorials/T011_query_online_api_webservices.nblink
    talktorials/T012_query_klifs.nblink
+   talktorials/T015_protein_ligand_docking.nblink
    talktorials/T016_protein_ligand_interactions.nblink
diff --git a/docs/talktorials.rst b/docs/talktorials.rst
@@ -49,6 +49,7 @@ Structural biology
    talktorials/T009_compound_ensemble_pharmacophores.nblink
    talktorials/T010_binding_site_comparison.nblink
    talktorials/T012_query_klifs.nblink
+   talktorials/T015_protein_ligand_docking.nblink
    talktorials/T016_protein_ligand_interactions.nblink
 
 

diff --git a/docs/talktorials/T015_protein_ligand_docking.nblink b/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"]}
diff --git a/environment.yml b/environment.yml
@@ -32,6 +32,7 @@ dependencies:
   - redo
   - requests-cache
   - suds-community
+  - smina
   ## CI tests
   # Workaround for https://github.com/computationalmodelling/nbval/issues/153
   - pytest 5.*

diff --git a/teachopencadd/talktorials/T015_protein_ligand_docking/README.md b/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/)
diff --git a/teachopencadd/talktorials/T015_protein_ligand_docking/images/docking_workflow.png b/teachopencadd/talktorials/T015_protein_ligand_docking/images/docking_workflow.png
diff --git a/...ncadd/talktorials/T015_protein_ligand_docking/images/protein_ligand_complex.png b/...ncadd/talktorials/T015_protein_ligand_docking/images/protein_ligand_complex.png
diff --git a/teachopencadd/talktorials/T015_protein_ligand_docking/talktorial.ipynb b/teachopencadd/talktorials/T015_protein_ligand_docking/talktorial.ipynb