T025 Kinase similarity: KiSSim fingerprint

[dominiquesydow]

Description

• Talktorial ID: T025
• Title: Kinase similarity: Pocket structure (KiSSim)
• Original authors: @dominiquesydow
• Reviewer(s): @t-kimber, @AndreaVolkamer
• Date of review:

https://app.reviewnb.com/volkamerlab/teachopencadd/pull/121

Todos

Content

• Theory
  • Kinase dataset
  • Kinase similarity descriptor: XXX
• Practical
  • Retrieve and preprocess data
  • Show kinase coverage
  • Compare kinases
  • Save kinase distance matrix
  • Visualize similarity as kinase matrix > in T028
  • Visualize similarity as phylogenetic tree > in T028

Content review

• Potential labels or categories (e.g. machine learning, small molecules, online APIs): kinase, similarity, binding site
• One line summary: Assess kinase similarity based on kinase pocket structure
• The table of contents reflects the talktorial story-line; order of #, ##, ### headers is correct
• URLs are linked with meaningful words, instead of pasting the URL directly or linking words like here.
• I have spell-checked the notebook
• Images have enough resolution to be rendered with quality, without being too heavy.
• All figures have a description
• Markdown cell content is still in-line with code cell output (whenever results are discussed)
• I have checked that cell outputs are not incredibly long (this applies also to DataFrames)

Code review

• Time it took to execute (approx.):
• Variable and function names follow snake case rules (e.g. a_variable_name vs aVariableName)
• Spacing follows PEP8 (run Black on the code cells if needed)
• Code line are under 99 characters each (run black -l 99)
• Comments are useful and well placed
• There are no unpythonic idioms like for i in range(len(list)) (see slides)
• All 3rd party dependencies are listed at the top of the notebook
• I have marked all code cell with output referenced in markdown cells with the label # TODO: CI
• I have identified potential candidates for a code refactor / useful functions
• All import ... lines are at the top (practice part) cell, ordered by standard library / 3rd party packages / our own (teachopencadd.*)
• I have update the relative paths to absolute paths.
• List here unfamiliar libraries you find in the imports and their intended use: -

Questions

None.

Status

• Ready to go

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