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Docking studies for all gernerated protonation states were made using PLANTS and Gold with standard settings.
Docking studies for 3405 molecules of combinatorial library were carried out against AChE and BACE-1.
Furthermore, the high selectivity of 14c, e for Cdc7 over Rho-associated protein kinase 1 (ROCK1) is discussed by utilizing a docking study with Cdc7 and ROCK2 crystal structures.
This study successfully applied virtual screening for hit discovery, and a docking study for hit optimization.
The docking study for compound 3 is given in Figures 5(a) and 5(b).
We previously verified[ 24] the suitability of the crystal structure for use in docking studies by removing the cocrystallised androstenedione from the substrate binding site and using the docking program GOLD[ 51] to dock the steroid back in.
In the current study, Gold docking program was utilized to conduct extensive docking studies against the target crystal structure to develop a robust and predictive docking protocol.
A series of symmetrically bis-substituted imidazole analogs bearing at the N-1 and N-3 two biphenyl moieties ortho substituted either with tetrazole or carboxylate functional groups was designed based on docking studies and utilizing for the first time an extra hydrophobic binding cleft of AT1 receptor.
The Schrodinger Induced Fit Docking Extended Sampling protocol67,68 was used for docking studies of PIP2 on the optimized Kv7.2 configuration.
The binding mode of compound 88 to tubulin was also investigated utilizing a molecular docking study.
For the binding pose predictions, the recently reported X-ray crystal structure of mPGES-1 with the co-crystallized ligand (PDB code: LVJ; PDB accession code: 4bpm) was utilized for the docking study.
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