Sentence examples for docked compound from inspiring English sources

When comparing the binding interaction between clusters in Figures 3c, d, e, f, and g we noted that our method could cluster docked compound poses into distinct clusters revealing specific binding interactions and important protein-ligand interactions.

The docking study of the docked compound 3 into the active binding pocket of the human gamma-aminobutyric acid receptor showed arene-hydrogen interaction with bond length of 4.07 Å with binding energy of −3.2 kcal/mol with Thr202 of the receptor (Fig. 7c).

This protocol uses a high-throughput docking program to initially orient and score the ZINC fragment-like compounds in the binding site, and subjects the best single docking pose for each docked compound to a rescoring stage in which the ligand is energy minimized and the binding affinity is estimated using an all-atom molecular mechanics force field combined with an implicit solvent model.

The ROC-plot for the combined performance of the optimised receptor ensemble was computed by taking the best ICL VLS docking score of the receptor models for each docked compound.

The screening was accomplished using a computer docking program, DOCK, that docked each chemical of the database into the active sites of the enzymes and evaluated the shape complementarity of the docked compound relative to the active sites.

Figure 7 Binding site surface with docked, compound H5 (colored magenta).

The W279 also attain the similar conformation as in donepezil bound crystal structure (1EVE), which is in accordance with the Zn1 and Zn2 docked compounds.

DOI: http://dx.doi.org/10.7554/eLife.00857.036 The docked compounds were filtered based on the following criteria: (1) The docking models with a compound-fiber van der Waals attractive energy > −7.0 kcal/mol were removed; (2) The docking models with a compound-fiber hydrogen-binding energy >−0.2 kcal/mol were eliminated.

Docked compounds were ranked based on the GOLD score, which represents the sum of receptor ligand hydrogen bonding energy, van der Waals energy, torsional energy, and hydrophobic interaction energies and ranged from 66 to 36.

In contrast, the model based on the P2Y12R– 34 template was not efficient in docking compound 6 or its derivatives, as it did not yield any high-scoring binding conformations.

The receptor-based 3D-QSAR models were also derived using bioactive conformations obtained by docking compounds to the active sites of CAII.