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.
Our current model for DOCK-ELMO function in embryogenesis is shown in Figure 8.
The absence of the crystal structure for LdAdk prompted us to generate a 3D model for docking studies.
In preparing the enzyme's structure model for docking, this ligand was removed, leaving the heme unoccupied.
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.
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.
Dr. Hugo Gutiérrez-de-Terán is thanked for providing the A1R homology model for molecular docking studies.
Based on the crystal structure, we propose a model for C20 docking to the actin subunit at the pointed end.
As such, it represents an excellent starting model for the docking of small molecules that either inhibit or activate sGC.
