Docking simulations of the ligands in the FXR active site were carried out using Glide docking in the Schrodinger suite. The grid file were generated to the receptor by the position of the co-crystallized ligand. The grid size were 10 Å × 10 Å × 10 Å of inner box and 20 Å × 20 Å × 20 Å of outer box. The OPLS_2005 force field was used for grid generation. To accomplish the molecular docking, the extra precision (Glide XP) protocol was selected with ligands docked flexibly.
Glide docking
Manufactured by Schrödinger
Sourced in United States
Glide docking is a computational tool for predicting the binding modes and affinities of small molecules to protein targets. It uses a proprietary scoring function and search algorithm to efficiently explore the conformational space of the ligand-protein complex. The core function of Glide docking is to provide a reliable and accurate method for virtual screening and lead optimization in drug discovery projects.
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Lab products found in correlation
5 protocols using glide docking
1
Ligand Docking in FXR Active Site
2
NCI Compound Screening for SHP2 Inhibition
3
Large-Scale Molecular Docking with OpenEye HYBRID and Glide
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For large scale docking studies utilizing over 100,000 structures, OpenEye’s HYBRID Dock was used. HYBRID docking was done in parallel on all PNCK grids in one job thus aggregation of scores was not necessary as HYBRID only reports the highest scoring pose per compound per grid. The top 25,000 docking poses were exported for final analysis. For smaller scale docking jobs or confirmatory docking studies prior to MD simulation, Glide Docking was used (Schrödinger Release 2019–1 : Glide, Schrödinger, LLC, New York, NY, 2019). All default settings were used. Glide standard precision docking (SP) was performed using 3D ligands generated from LigPrep. Up to 25 poses were generated per ligand with the top 5 poses being selected for output. Glide scores were exported for aggregation across various grids using Pipeline Pilot.
4
Fragment-Based Docking with Induced Fit
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Docking was computed using Induced Fit Docking workflow of Schrödinger employing SP-setting for Glide docking (Glide, Schrödinger, LLC, New York, NY, 2020) and side chains 5 Å from initiative ligand poses were consider for conformational refinement with Prime module. At both stages of docking hydrogen bond was required to hinge amine of Met769. Graphical illustrations are made using PyMOL Molecular Graphics System, Version 2.4.1. Schrödinger, LLC.
5
Ligand Binding Site Identification for Mouse-Type T1R1
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The SiteMap program (Schrödinger, LLC) was used to initially identify two potential ligand binding sites for the mouse-type human T1R1; one was near the three mutated residues at the bottom of the binding site, and the other was in the upper region of the allosteric pocket. Glide docking (Schrödinger, LLC) was then performed to allow methional to explore both of these potential binding sites. Standard precision (SP) mode and the OPLS3 force field were used during docking.
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