laylagerami / addenbrookes_project

Renan and Layla's Addenbrooke's Project Files - Designing a selective and potent PDGFR-alpha inhibitor for fluorescent tagging and use as a PET tracer
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addenbrookes_project

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Pharmacophore modelling

PDGFR-a

Loaded 5grn.pdb into Schrodinger and ran preparation (all default, except I deleted Cl atoms and remove waters with less than 1 H-bonds to non-waters, added missing side chains).

Saved file as 5grn_prepared.pdb.

Tasks -> Develop Pharmacophore Model, create pharmacophore model using -> Receptor-ligand complex

CSF1R

Import pdb 6T2W and prepare. Added missing side chains. Deleted SO4 ions. Remove waters with less than 1 H-bonds to non waters. Everything else default.

Saved file as 6t2w_prepared.pdb

Tasks -> Develop Pharmacophore Model, create pharmacophore model using -> Receptor-ligand complex