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By using computational docking tools to construct a compendium of quaternary structural models, it becomes feasible to interrogate which of the models, with similar energy scores, are correct by using experimentally derived distance constraints.
Computational protein docking tools such as Rosetta have recently seen improvements5 but are generally applied to small quaternary structures supported by existing experimental structures of the individual proteins for which tertiary structures remain similar in the bound and unbound form.
NMR spectroscopy and computational docking have been recognized as an important tool for the interaction study of CDs-drug inclusion complexes in solution state.
Computational docking of substrates and reaction intermediates to Pa5106 was performed using Autodock Vina with the MGL tools 1.5.4 plugin.
The variety of Smac peptides was filtered by computational docking.
Thus, computational docking alone misses important prospective drug design leads.
Computational docking studies showed that the most active hybrids dock well within the binding site of HGPRT protein.
Computational docking calculations were done using GLIDE in standard precision (SP) mode [66] for flexible docking.
Molecular modeling studies were accomplished using Glide docking tool.
For this reason, we performed computational docking analysis of OT molecules in OTR binding sites.
Computational docking studies were performed with GOLD 4.1 (The Cambridge Crystallographic Data Centre [24], [25]).
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