Homology model of feline coronavirus UU16 was build based on electron-microscopy structure of human coronavirus NL63 spike protein (PDB ID: 5SZS (Walls et al., 2016 (link)) using the Prime program version 4.2 (Schrödinger, 2015 ) in Schrodinger software platform. Missing loops of SARS-CoV-2 spike protein was modeled also using the Prime program based on structure with PDB ID: 6VYB (Walls et al., 2020 (link)).
Prime program
Manufactured by Schrödinger
Sourced in United States
The Prime program is a computational platform that enables the rapid and accurate prediction of the properties of small molecules. It utilizes advanced algorithms and computational power to model and analyze the behavior of chemical compounds. The core function of the Prime program is to provide researchers and scientists with a tool to efficiently evaluate and optimize the characteristics of potential drug candidates or other small-molecule compounds.
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Lab products found in correlation
4 protocols using prime program
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Feline Coronavirus Spike Protein Homology
2
Molecular Docking Analysis of HCs-Cx46-CBX/ENX
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The HCs-Cx46-CBX/ENX interaction analysis was performed in the AutoDock Vina v1.2.3 program [73 (link)]. The interaction parameters were made keeping the protein rigid and the ligands as flexible molecules. In addition to this, a screening box or “Grid Box” with specific dimensions centered on the “interaction pocket” was generated using the AutoDock tools program. The generated complexes were classified according to the affinity constants predicted in kcal/mol. The analysis of the HCs-Cx46-CBX/ENX interface and the energetic parameters were performed in the Maestro program (Schrödinger, LLC, New York, NY, USA, 2016). Additionally, the theoretical Δgbind was calculated through the MM-GBSA energy calculation using the Prime program (Schrödinger, LLC, New York, NY, USA, 2016). All images were created in PyMOL v1.7 [107 ].
3
Induced Fit Docking of BRBEs Ligands
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Induced Fit Docking (IFD) module with Prime program of Schrodinger software package was used for docking analyses of the six ligands of BRBEs, COG, FLS, PCA, SYA, SPA, and pCmA with the target enzyme. In the Induced Fit protocol various ligand poses were generated temporarily eliminating highly flexible side chains during the docking step. These were subjected to energy minimization and finally, each ligand is re-docked into its corresponding low energy protein structures and the resulting complexes are positioned according to Glide Score.
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Refining Docking Poses with MM/GBSA
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All docking poses were rescored with the MM/GBSA approach, as implemented in the Prime program in the Schrödinger software suite [32 , 41 ]. It employed a single minimised protein–ligand structure, thus establishing an efficient approach to rapidly refine and rescore docking results. We employed the variable dielectric solvent model VSGB 2.0 [52 (link)], which includes empirical corrections for modelling directionality of hydrogen-bond and π-stacking interactions. This approach has been shown to give good binding free energies for a wide range of protein–ligand complexes [53 (link)]. Residues within 5.0 Å of the ligand were allowed to relax during the MM minimisation of the complex, keeping the rest of the structure fixed.
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