About the ready-made script...

HIV-1 protease resistance prediction

Few notes about it

Modeling mutants was performed in two steps:

  1. A search for the crystal structure with the highest identity to the mutant sequence using our database
  2. Building our model by replacing each mutant using the PLOP's algorithm.

Mutations were introduced simultaneously in the two protease chains and all systems were prepared with Schrödinger’s Protein Wizard. To map the protein-ligand conformational sampling we used PELE.