I am looking to identify/predict the probable mechanism of a particular compound with nuclear receptors. As docking studies are prone to false positive binding to multiple receptors, which docking software/ algorithm is most widely accepted for such predictions.
Also please elaborate on how to interpret the binding energies obtained for the liagnd among different receptors. Looking forward to interesting answers and discussions.
I would evaluate the receptor-ligand complexes by calculating relative ligand binding free energies using linear interaction energy (LIE) or linear response approximation (LRA) methods; more precise distinguishing between very similar ligands can be obtained with the rigorous free energy perturbation (FEP) method; all these methods are implemented in the Q molecular dynamics simulation package:
http://xray.bmc.uu.se/~aqwww/q/
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