Sentence examples for model for docking from inspiring English sources

In addition, we coded another option that uses the polar-hydrogen model for docking and then adds non-polar hydrogens to docked ligands for rescoring.

In preparing the enzyme's structure model for docking, this ligand was removed, leaving the heme unoccupied.

The absence of the crystal structure for LdAdk prompted us to generate a 3D model for docking studies.

Such techniques for modeling have shown to yield successful results through analysis of model 5-HT2 A (GPCR) receptors and use of the model for docking studies to identify ligand binding sites.

The protein preparation wizard from Maestro (Schrödinger Suite 2010 Protein Preparation Wizard; Epik version 2.1, Schrödinger, LLC, New York, NY, 2010; Impact version 5.6, Schrödinger, LLC, New York, NY, 2010; Prime version 2.2, Schrödinger, LLC, New York, NY, 2010) was used to prepare the receptor model for docking and to define docking boxes.

This is likely due to the fact that extracellular loops 1 and 2 (ECL1 and ECL2) are not resolved in the structure of the P2Y12R– 34 template, leaving the expected binding pocket widely open and incomplete and rendering the homology model unsuitable for docking new ligands (see Discussion).

Our current model for DOCK-ELMO function in embryogenesis is shown in Figure 8.

The output from AutoDock was used for docking model studies with PyMOL software (Smith et al. 2004).

In order to investigate the thrombin recognition of the most active and selective compounds, a molecular modeling study has been performed using available Protein Data Bank (PDB) structures as receptor models for docking experiments.

The X-ray structures of BsFtsZ [Protein Data Bank (PDB) entry 2RHL, A chain] and SaFtsZ (PDB entry 4DXD) were used as models for docking analysis.

The main challenge will be to accurately predict the conformations of the MHC residues that contact the peptide, particularly if a rigid model of the MHC is employed for docking.