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Fig. 2.
Flowchart of the docking procedure used in this work.
3.4.3.1 Rigid Docking of Residues at the Ends of Binding Groove
The main problem in docking simulation is to enumerate the number of combinations
for two molecules within an enclosed sampling space. There are six degrees of global-
rotational and translational freedom of one molecule relative to the other, as well as
one internal dihedral rotation per rotational bond. A full search on the conformational
space increases exponentially with increasing molecule size and sampling space. As
such, a key challenge in pMHC docking simulation is to minimize the conformational
search space of ligand within the large sampling space enclosed by the MHC binding
groove. A possible approach is to identify suitable base or anchor fragments (herein
referred to as probes) for initiating docking simulations. A probe must satisfy two
criteria: (i) the anchor must have sufficient contact with the receptor and (ii) the
