There is still a caveat, since the docking programs, primarily used in VS, may perform poorly on new targets, if they are different from their training sets.
The enzyme retains approximately 10% of the steady state oxidase activity using the artificial electron donor TMPD, but has no activity using the physiological electron donor cytochrome c4, since the docking site for this cytochrome is presumably located on the absent domain of CcoP.
Since the docking software accepts only one molecule at a time, we evaluated the combination effect using a "linked-structure" approach.
Since the docking protocol utilizes the rigidity in the protein conformation, it is thus essential to get account of the dynamicity for active site residues in association with the flexibility of chemical moieties.
Since the docking force fields involve "pure" ligand-based terms to calculate the binding energy for each ligand, we analyzed the contribution of the ligand internal energy to the final score for Autodock simulations.
Since the docking of different ligands with different complexity also leads to different runtimes and, thus, to different results of the average time, our further analyses are based on the measures for the whole dataset.
Since the docking results proved that the amino acid residues Asn132, Glu166, Pro167, Val172, Lys234 and Thr235 of CTX-M-15 (enzyme) make important contacts with cefotaxime (drug) in the 'enzyme-drug complex', researchers are expected to duly utilize this information for designing more potent and versatile CTX-M-inhibitors.
(iii ) Since the docking results proved that the amino acid residues Asn132, Glu166, Pro167, Val172, Lys234 and Thr235 of CTX-M-15 (enzyme) make important contacts with cefotaxime (drug) in the 'enzyme-drug complex', researchers are expected to duly utilize this information for designing more potent and versatile CTX-M-inhibitors.
There was a time that the Republican Party stood for fiscal restraint, but that boat has long since left the dock.
