Protein-Ligand Complex Stability Analysis

The Prime Molecular Mechanics-Generalized Born area MM-GBSA tool of Maestro 13.5, Schrödinger Suite 2022-3 is accustomed to determining the steadiness of the protein–ligand complexes according to their binding free energy. The ligands were prepared beforehand using LigPrep, and the relevant proteins were prepared using the protein preparation wizard, as detailed by the MM-GBSA technology available with Prime [45 (link)]. Sitemap anticipated the active sites of the proteins. Glide standard precision (SP) docking was then accustomed to dock the chemicals with proteins. The MM-GBSA technology offered with Prime was utilized to find the binding free energy of the ligand–protein complexes utilizing the Prime MM-GBSA panel. The OPLS3 physical phenomenon was chosen, and therefore the continuum solvent model was VSGB. The default settings for the opposite options were selected.

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Onikanni S.A., Lawal B., Munyembaraga V., Bakare O.S., Taher M., Khotib J., Susanti D., Oyinloye B.E., Noriega L., Famuti A., Fadaka A.O, & Ajiboye B.O. (2023). Profiling the Antidiabetic Potential of Compounds Identified from Fractionated Extracts of Entada africana toward Glucokinase Stimulation: Computational Insight. Molecules, 28(15), 5752.

Publication 2023

Maestro 13.5

Born Dock Ligand binding protein Ligands Mechanics Physical phenomenon Proteins Solvent

Corresponding Organization : Federal University Oye Ekiti

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Variable analysis

independent variables

The ligands prepared using LigPrep
The proteins prepared using the protein preparation wizard

dependent variables

The binding free energy of the ligand–protein complexes determined using the Prime MM-GBSA tool

control variables

The OPLS3 force field
The VSGB continuum solvent model
The default settings for the other options

controls

No positive or negative controls were explicitly mentioned in the information provided.

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