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Exact(19)
Each multi-conformer peptide-ligand was exhaustively docked to a receptor using default step-sizes and the ChemGauss2 scoring function (a propriety function of OpenEye) [41].
The reduced set of conformers may subsequently be docked to a protein structure and scored with more resource-intensive, but more accurate methods.
The ligands for the PARP example (Figure 5) were taken from the ZINC database [14] and docked to a protein provided by the PDB (PDB code: 1EFY).
In this mode, energy grids of all atom types are loaded and a block of N ligands are sequentially docked to a receptor.
The ligands were taken from the ZINC database [14] and docked to a protein provided by the PDB (PDB code: 1EFY).
Molecular modeling of these alkaloids docked to a homology model of Pgp was employed to optimize ligand protein interactions and design analogues with increased affinity to Pgp.
Similar(41)
As no obvious clash could be identified during docking to an α4β2 homology model, it appears that AChBP is not a strong predictor of α4β2 structure, perhaps reflecting different docking pathways or an altered binding site structure.
On average, only 37.39% of the ligands were docked to reach an accuracy level of (sim) 94%.
HIV initiates its infectious cycle by docking to CD4 and a chemokine receptor, most commonly CCR5.
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This month, there was a three-hour paddle from the clubhouse dock to a grassy patch of marshland a mile and a half offshore.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.
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CEO of Professional Science Editing for Scientists @ prosciediting.com