Sentence examples for by using ensemble docking from inspiring English sources

Regarding the sampling aspect, protein flexibility could be partially considered by using ensemble docking or induced-fit docking strategies.

However, our docking model was insufficient to specifically identify VDR antagonists and thus, further investigation using ensemble docking (i.e., combinatorial docking using diverse series of conformations for antagonists as well as a collection of different conformations for the VDR binding site) will be necessary to better account for the flexibility of the binding site.

We hypothesized that this induced fit strengthens ADP binding and re-evaluated binding affinities of ADP for unacetylated and acetylated Lys23 ANT using ensemble docking.

Improving prediction accuracy could be achieved by using ensembles.

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].

To investigate the consequences of acetylation on ADP binding, we used an ensemble docking approach.

Molecular docking simulations were carried out by using two different docking algorithm implemented in CDOCKER (flexible docking) and AutoDock programs (rigid docking).

Benchmarks of docking programs are regularly released to compare their performance, whether by using semi-rigid docking (flexible ligand, rigid protein) [7 14], flexible docking (flexible ligand and protein) [15 17], ensemble docking (using several conformations of the protein) [15, 18] or cross-docking (docking ligands taken from some structures on proteins from other structures) [19, 20].

The potential anti-angiogenesis targets of Lenalidomide derivatives were virtual screened on Auto-Dock 4.0 by using reverse docking method.

These residues were subsequently tested by using different docking spheres.

Bold p-values indicate a statistically significant performance improvement by using an ensemble causal orientation.