Merge pull request #115 from volkamerlab/kinase-talkorials

Base branch for new kinase talkorials

docs/all_talktorials.rst

@@ -28,3 +28,9 @@ This is the complete list of talktorials available for online reading. Take into
    talktorials/T020_md_analysis.nblink
    talktorials/T021_one_hot_encoding.nblink
    talktorials/T022_ligand_based_screening_neural_network.nblink
+   talktorials/T023_what_is_a_kinase.nblink
+   talktorials/T024_kinase_similarity_sequence.nblink
+   talktorials/T025_kinase_similarity_kissim.nblink
+   talktorials/T026_kinase_similarity_ifp.nblink
+   talktorials/T027_kinase_similarity_ligand_profile.nblink
+   talktorials/T028_kinase_similarity_compare_perspectives.nblink

docs/talktorials.rst

@@ -25,9 +25,10 @@ Talktorials as presented in the original `JCIM 2019 article <https://jcheminf.bi
 Ligand-based cheminformatics
 ----------------------------
 
+The basis for computer-aided drug discovery
+
 .. nbgallery::
    :name: ligandbased
-   :caption: The basis for computer-aided drug discovery
 
    talktorials/T001_query_chembl.nblink
    talktorials/T002_compound_adme.nblink
@@ -44,9 +45,10 @@ Ligand-based cheminformatics
 Structural biology
 ------------------
 
+3D models, structural similarity, protein-ligand interaction analysis and other methods
+
 .. nbgallery::
    :name: structuralmodeling
-   :caption: 3D models, structural similarity, protein-ligand interaction analysis and other methods
 
    talktorials/T008_query_pdb.nblink
    talktorials/T009_compound_ensemble_pharmacophores.nblink
@@ -64,13 +66,30 @@ Structural biology
 Online APIs/servers
 -------------------
 
+Online API/servers for structural bioinformatics and cheminformatics
+
 .. nbgallery::
    :name: onlineapi
-   :caption: Online API/servers for structural bioinformatics and cheminformatics
 
    talktorials/T001_query_chembl.nblink
    talktorials/T008_query_pdb.nblink
    talktorials/T011_query_online_api_webservices.nblink
    talktorials/T012_query_klifs.nblink
    talktorials/T013_query_pubchem.nblink
 
+
+Kinase similarity
+-------------------
+
+Kinase similarity comparison using various methods
+
+.. nbgallery::
+   :name: kinasesimilarity
+
+   talktorials/T023_what_is_a_kinase.nblink
+   talktorials/T024_kinase_similarity_sequence.nblink
+   talktorials/T025_kinase_similarity_kissim.nblink
+   talktorials/T026_kinase_similarity_ifp.nblink
+   talktorials/T027_kinase_similarity_ligand_profile.nblink
+   talktorials/T028_kinase_similarity_compare_perspectives.nblink
+

docs/talktorials/T023_what_is_a_kinase.nblink

@@ -0,0 +1 @@
+{"path": "../../teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb", "extra-media": ["../../teachopencadd/talktorials/T023_what_is_a_kinase/images"]}

docs/talktorials/T024_kinase_similarity_sequence.nblink

@@ -0,0 +1 @@
+{"path": "../../teachopencadd/talktorials/T024_kinase_similarity_sequence/talktorial.ipynb", "extra-media": ["../../teachopencadd/talktorials/T024_kinase_similarity_sequence/images"]}

docs/talktorials/T025_kinase_similarity_kissim.nblink

@@ -0,0 +1 @@
+{"path": "../../teachopencadd/talktorials/T025_kinase_similarity_kissim/talktorial.ipynb", "extra-media": ["../../teachopencadd/talktorials/T025_kinase_similarity_kissim/images"]}

docs/talktorials/T026_kinase_similarity_ifp.nblink

@@ -0,0 +1 @@
+{"path": "../../teachopencadd/talktorials/T026_kinase_similarity_ifp/talktorial.ipynb", "extra-media": ["../../teachopencadd/talktorials/T026_kinase_similarity_ifp/images"]}

docs/talktorials/T027_kinase_similarity_ligand_profile.nblink

@@ -0,0 +1 @@
+{"path": "../../teachopencadd/talktorials/T027_kinase_similarity_ligand_profile/talktorial.ipynb", "extra-media": ["../../teachopencadd/talktorials/T027_kinase_similarity_ligand_profile/images"]}

docs/talktorials/T028_kinase_similarity_compare_perspectives.nblink

@@ -0,0 +1 @@
+{"path": "../../teachopencadd/talktorials/T028_kinase_similarity_compare_perspectives/talktorial.ipynb", "extra-media": ["../../teachopencadd/talktorials/T028_kinase_similarity_compare_perspectives/images"]}

teachopencadd/talktorials/T023_what_is_a_kinase/README.md

@@ -0,0 +1,49 @@
+# T023 · What is a kinase?
+
+Authors:
+
+- Dominique Sydow, 2021, [Volkamer lab, Charité](https://volkamerlab.org/)
+- Talia B. Kimber, 2021, [Volkamer lab, Charité](https://volkamerlab.org/)
+- Andrea Volkamer, 2021, [Volkamer lab, Charité](https://volkamerlab.org/)
+
+
+## Aim of this talktorial
+
+In this talktorial, we will talk about kinases: why are they important in life and drug design, what do they look like, and what data resources are available?
+Finally, we select a set of kinases which will be analyzed in the forthcoming talktorials **T024**-**T028** with respect to their similarity, the goal being to gain insight into potential off-target effects.
+
+
+### Contents in *Theory*
+
+- Kinases in a nutshell
+    - The human kinome
+    - Kinase structures and important motifs
+- Kinase resources
+    - Kinase structures and related information
+    - Bioactivity data
+- Kinase similarity: Off-targets and promiscuous binding
+- Kinase dataset compilation
+
+
+### Contents in *Practical*
+
+- Define the kinases of interest
+
+
+### References
+
+- Kinases as drug targets: [<i>Nat. Rev. Drug Discov.</i> (2021), <b>20(7)</b>, 551-569](https://doi.org/10.1038/s41573-021-00195-4)
+- Sequence-based kinase clustering: Manning et al. [<i>Science</i> (2002), <b>298(5600)</b>, 1912-1934](https://doi.org/10.1126/science.1075762)
+- KinMap: 
+  - Paper: [<i>BMC Bioinformatics</i> (2017), <b>18</b>, 16](https://dx.doi.org/10.1186%2Fs12859-016-1433-7)
+  - Website: http://www.kinhub.org/kinmap/
+- KLIFS
+  - KLIFS URL: https://klifs.net/
+  - KLIFS database: [<i>Nucleic Acid Res.</i> (2020), <b>49(D1)</b>, D562-D569](https://doi.org/10.1093/nar/gkaa895)
+  - KLIFS binding site definition: [<i>J. Med. Chem.</i> (2014), <b>57(2)</b>, 249-277](https://doi.org/10.1021/jm400378w)
+- Bioactivity data
+  - Karaman et al. dataset: [<i>Nature Biotechnology</i> (2008), <b>26</b>, 127-132](https://doi.org/10.1038/nbt1358)
+  - Davis et al. dataset: [<i>Nature Biotechnology</i> (2011), <b>29</b>, 1046-1051](https://doi.org/10.1038/nbt.1990)
+  - KIBA dataset: [<i>J. Chem. Inf. Model.</i> (2014), <b>54(3)</b>, 753-743](https://doi.org/10.1021/ci400709d)
+  - PKIS dataset: [<i>PLOS ONE</i> (2017), <b>12</b>, 1-20](https://doi.org/10.1371/journal.pone.0181585)
+- Kinase selection: [<i>Molecules</i> (2021), <b>26(3)</b>, 629](https://www.mdpi.com/1420-3049/26/3/629)

teachopencadd/talktorials/T023_what_is_a_kinase/data/README.md

@@ -0,0 +1,6 @@
+# Data
+
+This folder stores input and output data for the Jupyter notebook.
+
+- `xxx.csv`: Describe data.
+- `xxx.sdf`: Describe data.

teachopencadd/talktorials/T023_what_is_a_kinase/data/kinase_selection.csv

@@ -0,0 +1,10 @@
+kinase,kinase_klifs,uniprot_id,group,full_kinase_name
+EGFR,EGFR,P00533,TK,Epidermal growth factor receptor
+ErbB2,ErbB2,P04626,TK,Erythroblastic leukemia viral oncogene homolog 2
+PI3K,p110a,P42336,Atypical,Phosphatidylinositol-3-kinase
+VEGFR2,KDR,P35968,TK,Vascular endothelial growth factor receptor 2
+BRAF,BRAF,P15056,TKL,Rapidly accelerated fibrosarcoma isoform B
+CDK2,CDK2,P24941,CMGC,Cyclic-dependent kinase 2
+LCK,LCK,P06239,TK,Lymphocyte-specific protein tyrosine kinase
+MET,MET,P08581,TK,Mesenchymal-epithelial transition factor
+p38a,p38a,Q16539,CMGC,p38 mitogen activated protein kinase alpha