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A novel method for fast and accurate prediction of ligand induced conformational changes in receptor active sites

The LXR-beta co-crystal structures corresponding to PDB structures 1PQ6 and 1P8D are shown at the top left and bottom left. The IFD result of inducing the larger 1PQ6 ligand into the smaller 1P8D receptor binding site is shown at right.

Induced Fit: A novel method for fast and accurate prediction of ligand induced conformational changes in receptor active sites

Schrödinger's innovative method for modeling the conformational changes induced by ligand binding. By merging the predictive power of Prime with the docking and scoring capabilities of Glide, Induced Fit is able to predict active site geometries with remarkable success.

About Induced Fit

The active site geometry of a protein complex depends heavily upon conformational changes induced by the bound ligand. However, resolving the crystallographic structure of a protein-ligand complex requires a substantial investment of time, and is frequently infeasible or impossible. Schrödinger's Induced Fit (IFD) protocol solves this problem by using Glide and Prime to exhaustively consider possible binding modes and the associated conformational changes within receptor active sites. The unique procedure allows chemists to quickly predict active site geometries with minimal expense, even for systems as challenging as hERG homology models.

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 Schrödinger 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.

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