In this study, molecular docking experiment was accomplished using the methods and parameters as suggested previously [44 ]. Preparation of three-dimensional structure of downloaded compounds was operated in LigPrep module of Schrödinger maestro (LigPrep, Schrödinger, LLC, New York, NY, 2017). Conversely, the receptors used for molecular docking namely Human estrogen receptor alpha (PDB id: 3ERT ) [45 (link)], Human gamma-aminobutyric acid receptor (PDB id: 4COF ) [46 ], Potassium channel (PDB id: 4UUJ ) [47 (link)], Human pancreatic alpha-amylase (PDB id: 4GQR ) [48 (link)] and Human tissue plasminogen activator (PDB id: 1A5H ) [49 (link)] were retrieved from RCSB Protein Data Bank [50 (link)] and prepared using protein preparation wizard in Schrödinger Maestro (Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2017). The active sites on target receptors were determined by PockDrug server, which estimates pocket druggability using ligand proximity method [51 ]. Finally, standard precision molecular docking was performed in Glide of Schrodinger maestro (v11.1) and expressed as glide score.
Protein preparation wizard epik
Manufactured by Schrödinger
The Protein Preparation Wizard; Epik is a software tool developed by Schrödinger for the preparation and optimization of protein structures. It performs tasks such as adding hydrogen atoms, assigning protonation states, and optimizing the protein's three-dimensional structure. The Protein Preparation Wizard; Epik is designed to prepare protein structures for further computational analysis and modeling.
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Lab products found in correlation
2 protocols using protein preparation wizard epik
1
Molecular Docking of Bioactive Compounds
2
Structural Modeling of Human Myo5c
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A structural model of the motor domain of human Myo5c (Uniprot–ID: Q9NQX4) was generated with AlphaFold2 version 2.3.1, the fasta file was accessed on 1 November 2023 (Jumper et al., 2021 (link)). Different conformers and tautomers of PBP [2,3,4–tribromo–5–(3,5–dibromo–2–hydroxyphenyl)–1H–pyrrole] were generated with QM Conformer and Tautomer Predictor of Jaguar (Jaguar, Schrödinger, LLC, New York, NY, 2023). PBP was inserted, with Glide, into the model of human Myo5c (Glide, Schrödinger, LLC, New York, NY, 2023.). The glide grid was generated in accordance to the position of PBP in the structure of the motor domain of Dictyostelium discoideum myosin–2 (PDB–ID: 2JHR). The PDB–structure was accessed on 11 October 2023. Analysis of the structural models and visualization of the results was done with Maestro in the Schrödinger Suite 2023–4 (Maestro, Schrödinger, LLC, New York, NY, 2023). The structure was prepared with the Protein Preparation Workflow and the minimization was done with the Minimization tool of Maestro (Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2023) for 200 cycles with 80 steps per cycle in the VSGB solvate model (Li et al., 2011 (link)). ΔG was calculated with the Prime MM–GBSA v3.000 tool for the minimized structure (Prime, Schrödinger, LLC, New York, NY, 2023).
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