Article ID: 185 - Last Modified: December 4, 2010
Does IFD change the backbone coordinates of my protein, or does it sample only side-chain orientations?
In the default mode, the largest changes in the IFD protocol are for side-chain rotameric states. However, after side-chain optimization, a backbone minimization is carried out to relax the protein structure in order to accommodate the new side-chain positions. So, small changes in the backbone are typically observed. On the other hand, it is possible to include a loop-optimization stage in the IFD workflow, which will explicitly vary the backbone coordinates of the selected protein segment.
Keywords: Induced fit, sampling, side-chain, backbone, IFD, loop
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