Homology modelling - Githubissues

openkinome / kinoml

Structure-informed machine learning for kinase modeling

https://openkinome.org/kinoml/

MIT License

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Homology modelling #26

Closed glass-w closed 3 years ago

glass-w commented 4 years ago

Description

This PR adds homology modelling functionality.

Todos

[ ] Preparation with MODELLER and MDAnalysis
- [x] retrieve canonical sequence from UniProt based on ID
  - [x] retrieve Kinase domain sequence from Uniprot with information about termini
- [x] obtain a PDB template via BLAST search
- [x] create properly formatted alignment file
  - [x] cut unnecessary residues
  - [ ] renumbering residues
  - [x] build missing residues
  - [x] add option for including ligands in template structure

Status

[ ] Ready to go

schallerdavid commented 4 years ago

Hey @WG150, I changed the base branch to docking. I think this way is cleaner, since the docking branch is some how our structure-based branch.

jaimergp commented 4 years ago

Tag me when needed!

glass-w commented 4 years ago

@jaimergp I have refactored this PR and would appreciate if you could give me some feedback. The general use case is now detailed in the notebook.