What is Induced Fit Docking and how can it help my research?

Schrödinger has developed and validated an Induced Fit Docking (IFD) protocol, based on Glide and the Refinement module in Prime, that accurately predicts ligand binding modes and concomitant structural changes in the receptor. A Python script automates the IFD protocol and offers a Maestro interface for specifying receptor and ligand structures and other settings.

Standard virtual docking studies assume a rigid receptor, but in reality many receptors alter their binding site to conform to the shape and binding mode of the ligand. This is often referred to as induced fit and is one of the main complicating factors in structure-based drug design.

The ability to model induced fit docking has two main applications:

• Generation of an accurate complex structure for a ligand known to be active but that cannot be docked in an existing (rigid) structure of the receptor.
• Rescue of false negatives (poorly scored true binders) in virtual screening experiments, where instead of screening against a single conformation of the receptor, additional conformations obtained from the IFD protocol are used.

For more information about the IFD protocol, including a tutorial, see the Induced Fit Docking manual. Protein and ligand structures for the IFD protocol must meet the requirements of both programs. For more information about Glide requirements, see the Glide User Manual.

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