Sentence examples for input for docking from inspiring English sources

Correlations between the binding constants and the predicted binding scores when native conformers were provided together with low-energy conformers as input for docking.

If the pair of monomers input for docking are initially placed too far apart, then the first local docking search performed may fail to locate them.

Hydrogen atoms and protonation states were automatically assigned using the Protonate 3D function of the Molecular Operating Environment Chemical Computing Groupp, Montreal, QC, Canada) [ 21], and the structures were saved in Mol2 file format, which was then used as input for docking analysis in rDock [ 22].

To the author's knowledge this is the first study where MOPAC2009 software is used for semi-empirical charge calculations on proteins systematically for preparing input files for docking calculations.

The restraints derived from the NMR experiments were used as input data for docking calculations for the human cytochrome c−Bcl-xL system with the program HADDOCK [19] and unequivocally define the interface on both proteins.

20 The active site residues (His257, Cys258, Gln259, Ala260, Gly261, Ile262, Ser263, and Arg264) of MKP1 and (Lys9, Ser10, and Lys14) of histone H3 were used as input parameters for docking.

Grid generated output file was uploaded as an input for Ligand docking against protein prepared targets in GLIDE.

The optimized geometry of the ligand is employed as input for subsequent docking, while the topology obtained is converted to GROMACS [31] format using ACPYPE [37].

Using omega-generated conformers as input for confined docking the ligand of the 1MQ6 X-ray structure was accurately reproducing the native pose of this ligand with a 1.8 Å RMSD to the X-ray pose (Figure 10C).

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).

2BID and 3E7O pdb structural files were used as input for analysis and docking simulations.