INSPIRE based plan for builder

Basic scaffold

• split ligand and protein
• apply biomt

Loop fill

Initial goals

• ParmEd + Modeller
• Single chain
• FASTA + PDB (later use PDB header)
• Fill multiple gaps
• Preserve numbering?

Stretch goals

• Multiple chains

Point mutation

• Need to ensure numbering is preserved relative to input

Template based builder

• basically full homology modelling

Kinase builder

Check if input is kinase

Library/database of structures

• biological identifiers
• bound ligands
• based on KLIFS database

Ligand handling

• smiles, pdb or mol2
• protonation?
• check database
• parameterize if unknown (or flag set)
• dock to give coordinates

Model Creator

Protein protonation states

• flag to indicate if pre-set

Create Amber topology (wrap leap)

Solvate

• ion concentration