Sentence examples for by using the docking from inspiring English sources
If this similarity can be demonstrated from CPI vectors, the efficacy of CPI could be broadened, e.g., the drug efficacy could be predicted by using the docking score vector of a drug towards multi-protein set.
In this way we evaluated the difference between the complex structure obtained by using the docking calculation and the X-ray crystal structure.
In this study we derived cutoff scores either by using the docking scores of the cocrystal structure ligands or by averaging the docking or weighted scores of all the ligands binding to the five crystal structures (Table 1).
Molecular modeling of trypsin OGp analogue complexes: All described molecular docking studies were performed by using the flexible docking program Fleksy.
We modeled the UDPGA and bilirubin binding of UGT1A1 by using the molecular docking program GOLD (Genetic Optimization for Ligand Docking) [ 63] with default genetic algorithm parameters.
By using the HADDOCK docking program (see Methods), we performed a docking simulation to explore further the possible structural arrangements that are compatible with the interface residues identified from the NMR and mutational analyses.
To improve the enantioconvergence of an epoxide hydrolase from Phaseolus vulgaris (PvEH1) towards styrene epoxides, its directed modification was performed based on the rational design by using the molecule docking simulation and the multiple alignment.
All the modeling processes are implemented by using the Symmetric Docking protocol in Rosetta software suite [ 17].
The MDock is automated molecular docking software for simultaneously docking dioscin with known/available three-dimension crystal structure against drug targets from PDTD with multiple protein structure/conformations downloaded from RCSB Protein Data Bank (PDB) by using the ensemble docking algorithm [ 24].
A W361F variant that showed higher hydrolytic activity for ginsenoside Rd than the wild-type SS-BGL was obtained by rational design using the docking pose interacting with Val209 among the ginsenoside Rd-docking SS-BGL models.
W361F was obtained by rational design using the docking pose that exhibited 4.2-fold higher activity, 3.7-fold higher catalytic efficiency, and 3.1-fold lower binding energy for Rd than the wild-type enzyme, indicating that W361F compensated for the limiting step.
