Sentence examples for binding poses in close from inspiring English sources
To evaluate PharmDock's performance in predicting ligand binding poses in close agreement with the X-ray poses, we performed cognate docking studies on the PDBbind [11, 15] core set.
We docked PXN into the ELIC pore and identified possible binding poses in two regions: above F16′ and close to position 6′.
Although triclosan displayed slightly altered binding poses in the different parasitic DHFRs, the inhibitor showed the same interactions with all four DHFRs, indicating comparable affinity (binding free energies in the range −7.24 and −7.56 kcal/mol).
An interesting feature of absolute calculations is the possibility to account for multiple binding poses in the final binding free energy estimate.
For the WT, mutants, and polymorphic variants, docking against the ensemble of molecular dynamics conformations identified native-like binding poses of ATP close to the previously reported crystal structure of the ATP-bound state.
The scoring functions are generally used in a qualitative manner to rank ligand binding poses and in doing so estimate the free energy of binding.
Predicted binding poses of triclosan (in purple) bound to the active site of DHFRs.
Possible binding poses were investigated by in silico modelling, providing a basis for optimisation of fragment binding and improved potency against NDH-2.
Orange: Ligand binding pose predicted in the unbiased docking setting with all identified protein-based pharmacophores.
This observed binding pose is in agreement with previously proposed binding modes for heparin on IL-8.
