The Induced Fit protocol begins by docking the active ligand with Glide. In order to generate a diverse ensemble of ligand poses, the procedure uses reduced van der Waals radii and an increased Coulomb-vdW cutoff, and can temporarily remove highly flexible side chains during the docking step. For each pose, a Prime structure prediction is then used to accommodate the ligand by reorienting nearby side chains. These residues and the ligand are then minimized. Finally, each ligand is re-docked into its corresponding low energy protein structures and the resulting complexes are ranked according to GlideScore. Accuracy is ensured by Glide's superior scoring function and Prime's advanced conformational refinement.
The Induced Fit methodology has been thoroughly refined in real-world research applications, and is readily used by novice and expert modelers alike. Maestro, the graphical user interface for all Schrodinger software, allows researchers to easily perform Induced Fit simulations and interpret the results. In addition to default settings suitable for a wide range of systems, the Induced Fit interface features advanced options that can be customized to solve more challenging cases. Calculations can be completed in a matter of hours on a desktop machine, or in as few as 30 minutes when distributed across multiple processors.
Software Link : Induced Fit - Ligand−Receptor Analysis Software