Merge pull request #118 from volkamerlab/tk-t027-kinsim-lig

T027 Kinase similarity: ligand-profile

teachopencadd/talktorials/T027_kinase_similarity_ligand_profile/README.md

@@ -0,0 +1,78 @@
+<div class="alert alert-block alert-info">
+
+<b>Thank you for contributing to TeachOpenCADD!</b>
+
+</div>
+
+
+<div class="alert alert-block alert-info">
+
+<b>Set up your PR</b>: Please check out our <a href="https://github.com/volkamerlab/teachopencadd/issues/41">issue</a> on how to set up a PR for new talktorials, including standard checks and TODOs.
+
+</div>
+
+
+# T000 · Talktorial topic title
+
+Authors:
+
+- First and last name, year(s) of contribution, lab, institution
+- First and last name, year(s) of contribution, lab, institution
+
+
+*The examples used in this talktorial template are taken from [__Talktorial T001__](https://github.com/volkamerlab/teachopencadd/blob/master/teachopencadd/talktorials/T001_query_chembl/talktorial.ipynb) and [__Talktorial T002__](https://github.com/volkamerlab/teachopencadd/blob/master/teachopencadd/talktorials/T002_compound_adme/talktorial.ipynb).*
+
+
+<div class="alert alert-block alert-info">
+
+<b>Cross-referencing talktorials</b>: If you want to cross-reference to existing talktorials in your notebook, please use the following formatting: <b>Talktorial T000</b>.
+
+</div>
+
+
+## Aim of this talktorial
+
+Add a short summary of this talktorial's content.
+
+
+### Contents in *Theory*
+
+_Add Table of Contents (TOC) for Theory section._
+
+* ChEMBL database
+* Compound activity measures
+
+
+<div class="alert alert-block alert-info">
+
+<b>Sync TOC with section titles</b>: These points should refer to the headlines of your <i>Theory</i> section.
+
+</div>
+
+
+### Contents in *Practical*
+
+_Add Table of Contents (TOC) for Practical section._
+
+* Connect to ChEMBL database
+* Load and draw molecules
+
+
+<div class="alert alert-block alert-info">
+
+<b>Sync TOC with section titles</b>: These points should refer to the headlines of your <i>Practical</i> section.
+
+</div>
+
+
+### References
+
+* Paper 
+* Tutorial links
+* Other useful resources
+
+*We suggest the following citation style:*
+* Keyword describing resource: <i>Journal</i> (year), <b>volume</b>, pages (link to resource) 
+
+*Example:*
+* ChEMBL web services: [<i>Nucleic Acids Res.</i> (2015), <b>43</b>, 612-620](https://academic.oup.com/nar/article/43/W1/W612/2467881) 

teachopencadd/talktorials/T027_kinase_similarity_ligand_profile/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/T027_kinase_similarity_ligand_profile/data/kinase_similarity_matrix_ligand_profile.csv

@@ -0,0 +1,10 @@
+,EGFR,ErbB2,BRAF,CDK2,LCK,MET,p38a,KDR,p110a
+EGFR,0.6089623445220651,0.5569176882661997,0.41935483870967744,0.11627906976744186,0.23846153846153847,0.22580645161290322,0.3157894736842105,0.3482142857142857,0.07142857142857142
+ErbB2,0.5569176882661997,0.6050767414403778,0.25,0.15384615384615385,0.17647058823529413,0.03571428571428571,0.125,0.39779005524861877,
+BRAF,0.41935483870967744,0.25,0.8115154807170016,0.06666666666666667,0.5116279069767442,0.1111111111111111,0.6444444444444445,0.7481203007518797,0.16666666666666666
+CDK2,0.11627906976744186,0.15384615384615385,0.06666666666666667,0.5441860465116279,0.16666666666666666,0.08695652173913043,0.08333333333333333,0.6016949152542372,0.26666666666666666
+LCK,0.23846153846153847,0.17647058823529413,0.5116279069767442,0.16666666666666666,0.605074821080026,0.2878787878787879,0.48936170212765956,0.4326923076923077,0.0
+MET,0.22580645161290322,0.03571428571428571,0.1111111111111111,0.08695652173913043,0.2878787878787879,0.7922722438851472,0.047619047619047616,0.5393586005830904,0.0
+p38a,0.3157894736842105,0.125,0.6444444444444445,0.08333333333333333,0.48936170212765956,0.047619047619047616,0.7647547797173733,0.5,0.0
+KDR,0.3482142857142857,0.39779005524861877,0.7481203007518797,0.6016949152542372,0.4326923076923077,0.5393586005830904,0.5,0.6967471143756558,0.1807909604519774
+p110a,0.07142857142857142,,0.16666666666666666,0.26666666666666666,0.0,0.0,0.0,0.1807909604519774,0.6395215090867264

teachopencadd/talktorials/T027_kinase_similarity_ligand_profile/images/README.md

@@ -0,0 +1,5 @@
+# Talktorial title
+
+## Images
+
+This folder stores images used in the Jupyter notebook.