Sentence examples for docking to generate from inspiring English sources
We use fragment docking to generate various e-pharmacophore hypotheses depicting protein residues important for ligand binding.
It consists of a series of Perl scripts that utilize the output of molecular docking to generate "site maps" of a protein binding site.
Notably, as discussed in methods "Virtual screening of DrugBank by 3D molecular docking", our consensus screening platform discarded inactive compounds after each round of docking to generate a set of "active" compounds with all three peptides P1, P2, and P3.
In some cases, MD simulations of the protein target have been carried out before docking to generate a conformer of the protein which differs from the available crystal structure(s).
A method called pyDockTET (tethered-docking) uses rigid-body docking to generate domain domain complexes that are scored by the electrostatic and desolvation energy terms, as well as a pseudo-energy term reflecting restraints from linker end-to-end distances; in this manner, near-native pair-wise domain poses are selected.
Finally, they performed computational docking to generate models of the gH1/NCP complex.
One critical part of ensemble docking is to generate an ensemble of peptide 3D models that include protein-bound peptide conformations, so that the biologically active ones can be selected by the protein during ensemble docking [3, 23, 28].
The structure of the ligand(s) must be processed to provide suitable 3D coordinates as input for molecular docking, and to generate the force-field potential parameters that will describe bonded and nonbonded interactions involving the ligand during MD (referred to as topology).
Finally, we use the docking results to generate a list of drug-target pairs where for a given pair the drug is expected to bind and influence the protein target.
Trimers were combined via docking software to generate three possible atomic structures of the TNH hexamer.
The experimental data were used with the HADDOCK ligand docking software to generate ligand protein structures, and the CORCEMA-ST protocol was used to predict STD intensities from the atomic coordinates of models for the ligand protein complex and to score the various LewisX DC-SIGN structures.
