FiberDock is a new method for flexible refinement of docking solution candidates. The method models both side-chain and backbone flexibility and performs rigid body optimization on the ligand orientation. The refinement algorithm mimics an induced fit process. The backbone and side-chain movements are modeled according to the binding van der Waals forces between the receptor and ligand. The method uses both low and high frequency normal modes and therefore is able to model both global and local conformational changes, such as opening of binding sites and loop movement. After refining all the docking solution candidates, the refined models are re-scored according to an energy function.
Here you can download an executable of FiberDock for Linux operating system.
This application is free for academic use.
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