We retrieved the structure of EGFR D770insNPG protein (Protein Data Bank: 4LRM) and used it as a template to build our molecular 3D structural model of EGFR D770insNPG. HER2 A775insYVMA was built using the previously published model in Shen et al52. The homology models were built using MODELLER 9v6 and were further energetically minimized using the Molecular Operating Environment software package (Chemical Computing Group, Montreal, Canada). Molecular docking of TKIs into exon 20 mutant EGFR and HER2 were performed using GOLD software with default parameters unless otherwise noted. No early termination was allowed in the docking process. Restraints were used to model the covalent bond formations between receptors and inhibitors. The flexibility of residues within the binding pocket was addressed using GOLD software. Figures demonstrating interactions between EGFR and/or HER2 and inhibitors were visualized using PyMOL.
Molecular operating environment software package
Manufactured by Chemical Computing Group
Sourced in Canada
Molecular Operating Environment (MOE) is a software package developed by Chemical Computing Group. It provides a comprehensive suite of tools for molecular modeling, simulation, and analysis. The core function of MOE is to enable users to study the structure, properties, and interactions of molecules, which is essential for a wide range of applications in the fields of chemistry, biology, and drug discovery.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using molecular operating environment software package
1
Molecular Modeling of EGFR and HER2 Exon 20 Mutants
2
Disulfide Bridge Simulation of TfCut2
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The disulfide bridge was introduced using the molecular operating environment software package (Chemical Computing Group, Montreal, Canada). The crystal structure of TfCut2 (PDB ID: 4CG1 ) was used as a template 11 . MD simulations were performed using the gromacs 5 software (Uppsala University, Uppsala, Sweden) adopting AMBER99SB force field parameters as described previously 14 . Equilibrations and MD simulations were carried out at 373 K. The probability densities of amino acid residues were calculated using GROMACS 5 excluding densities below 5% and those not present in all three rounds of simulation. Occupancy maps were calculated using the vmd 1.9.1 software package (University of Illinois, Champaign, IL, USA) using the same exclusion parameters as applied for the probability densities.
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