MutDTA

Improving the precision oncology pipeline by providing binding affinity purtubations predictions on a pirori identified cancer driver genes.

Current Progress

[ ] Data preprocessing
- [x] PDBbind - simple enough to use. Protein seq were downloaded from UniProt.
- [x] PLATINUM - Working on getting mutated sequence data (done with mutalyzer)
- [ ] KIBA and Davis - Kinase proteins are not super relevant but could be useful for pretraining since datasets are limited.
- [ ] GENIE - This will require some physical docking methods since we have no binding affinity data for this.
[x] Docking baseline
- [x] Set up Docking on cluster
- [x] Build scripts to automate ligand and protein prep (including grid for binding site).
- [x] Run docking on PDBbind dataset
[ ] Model baseline
- [ ] DGraphDTA
  - [x] Evaluate pretrained model on PDBbind dataset
  - [x] Train model on refined-set PDBbind dataset and evaluate
  - [ ] Train model on general PDBbind dataset and evaluate

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