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J Mol Graph Model. 2010 Nov;29(3):309-20. doi: 10.1016/j.jmgm.2010.09.008. Epub 2010 Oct 7.

DFG-in and DFG-out homology models of TrkB kinase receptor: induced-fit and ensemble docking.

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University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 1000 Ljubljana, Slovenia.


Kinases from the Trk family are important for the regulation of development and for the correct functioning of the neural system. Deregulation (over-expression) of Trks leads to survival and proliferation of different human cancers. Therefore, development of inhibitors for Trks that can disrupt the signal pathway of Trks could lead to cure against cancer as well as to nociception. Homology models built by YASARA have been used as targets for docking various libraries of known Trk inhibitors. The receptor plasticity was compensated with induced fit docking and/or ensemble docking. It was determined that DFG-in and DFG-out conformational states of TrkB kinase must be taken into account in order to get more reasonable relationships between the docking score and the activity measured by pIC₅₀ or the corresponding ligands.

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