The crystal structure (PDB ID: 6LZE) of SARS-CoV-2 Mpro, which was resolved by Dai et al. (Dai et al., 2020 (link)), was extracted from the RCSB Protein Data Bank (PDB). Then, the protein structure was prepared using the Protein Preparation Wizard module in Schrodinger 2017 (Bhachoo and Beuming, 2017 (link)) to remove all crystallographic water molecules, correct side chains with missing atoms, add hydrogen atoms and assign protonation states and partial charges with the OPLS_2005 force field. The Protein Preparation Wizard module of Schrödinger was applied to add hydrogen. The protonation states for the hydroxyl, Asn, Gln, and His were optimized using the ProtAssign module of Schrödinger. After that, the protein structure was minimized until the root-mean-square deviation (RMSD) of the nonhydrogen atoms reached less than 0.3 Å. The structures of the 15 natural compounds and 17 chemical compounds were prepared using the LigPrep module of the Schrodinger 2017 molecular modeling package to add hydrogen atoms, convert 2D structures to 3D, generate stereoisomers and determine the ionization state at pH 7.0 ± 2.0 with Epik. Using the prepared receptor structure, a receptor grid was generated around the original ligand site of the crystal structure. Then, the 15 natural compounds and 17 chemical compounds were docked to the receptor using the Glide XP protocol.
Protein preparation wizard module
Manufactured by Schrödinger
Sourced in United States
The Protein Preparation Wizard module is a tool designed for efficiently preparing protein samples for various analytical and experimental applications. It automates and streamlines the process of protein preparation, ensuring consistent and reliable results.
Automatically generated - may contain errors
Lab products found in correlation
Ligprep module, by Schrödinger (11 mentions)
Glide module, by Schrödinger (4 mentions)
Maestro, by Schrödinger (2 mentions)
Ligprep, by Schrödinger (2 mentions)
Pipeline pilot, by Dassault Systèmes (1 mentions)
Maestro v11, by Schrödinger (1 mentions)
2d sketcher, by Schrödinger (1 mentions)
Prime module, by Schrödinger (1 mentions)
Maestro version 11, by Schrödinger (1 mentions)
Grid generation module, by Schrödinger (1 mentions)
Receptor grid generation module, by Schrödinger (1 mentions)
Sitemap module, by Schrödinger (1 mentions)
Glide grid module, by Schrödinger (1 mentions)
Protein preparation wizard, by Schrödinger (1 mentions)
Macromodel, by Schrödinger (1 mentions)
Pymol molecular graphics system, by Schrödinger (1 mentions)
Prime mm gbsa module, by Schrödinger (1 mentions)
51 protocols using protein preparation wizard module
1
Structural Preparations for SARS-CoV-2 M^pro Docking
2
Binding Model of S. aureus NDH-2 and Entrectinib
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The molecular structure pdb file for S. aureus NDH-2 protein (5NA4) was downloaded from the Protein Data Bank (PDB). Using the Protein Preparation Wizard module of Schrödinger software to hydrogenate, repair missing residues, and optimize the structure, and water molecules. The molecular 3D structure file for entrectinib was downloaded from PubChem. The binding model of NDH-2 protein and entrectinib was predicted by molecular docking. Briefly, the best binding pocket of NDH-2 protein was chosen by structure-based cavity detection, then the docking based on AutoDockVina was performed to investigate the best binding site of entrectinib according to the Vina score (kcal/mol) in the pocket (Liu et al., 2022 (link)).
3
Preparation of Bromodomain-Containing Protein 4 Structure
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The apo crystal structure of CBP BrD was downloaded from the Protein Data Bank (PDB Code: 4OUF). Specifically, all of the solvent molecules, except conservative water (residue number: 1313), were removed, and only the A chain was retained. Subsequently, the remaining protein structure was prepared using the Protein Preparation Wizard module (Schrödinger, LLC, New York, NY, USA, 2017) in Maestro (Maestro, version 11.1; Schrödinger, LLC: New York, NY, USA, 2017) with standard Glide protocols [29 (link)], including assigning bond orders, adding hydrogens, creating disulfide bonds, and generating het states using Epik at pH 7.4 ± 2.0. Then, H-bond optimization and restrained minimization were performed with the OPLS3 force field and the default value for RMSD of 0.30 Å for converging heavy atoms. The receptor grid was defined as a closed box centered at crucial residues, including N1168, R1173, and Y1125, and other settings were set to default values.
4
Molecular Docking of ISL Compound
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The docking software was the Glide module of Schrödinger 2018 (Schrödinger, LLC, New York, USA). The crystal structure 1ZXM was processed by the Protein Preparation Wizard module of the Schrödinger software. The processing includes completing the missing side chain and loop region structure of the protein, removing all unbonded heteroatoms and water molecules, completing the missing hydrogen atoms, assigning protonated states and partial charges, and finally optimizing the protein structure using the OPLS3e force field until RMSD is optimized to a maximum value of 0.3 Å to reduce atomic space collisions. Next, a box of 20 Å × 20 Å × 20 Å centered on the center of mass of the ligand was identified as the docking area using the Receptor Grid Generation module, and the grid file for docking was generated.
The 3D structure of the small molecule, ISL, was preprocessed with the Ligprep module, and the protonated state was generated at pH = 7.0 ± 2.0. The prepared small molecule was then docked to the pocket using the Glide program in standard scoring mode (standard precision, SP).
The 3D structure of the small molecule, ISL, was preprocessed with the Ligprep module, and the protonated state was generated at pH = 7.0 ± 2.0. The prepared small molecule was then docked to the pocket using the Glide program in standard scoring mode (standard precision, SP).
5
Molecular Docking of hGCN5 Inhibitors
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The 2D-similarity based analogue searching was performed using Pipeline Pilot (version 7.5; Accelrys Inc., San Diego, CA, USA) as previously described.34 (link) Molecular docking studies were performed in order to analyze the binding modes of DC_HG24-01 and its derivatives. Firstly, the crystal structure of hGCN5 was fetched from the protein data bank (PDB code: 1Z4R ). The ligands were prepared by LigPrep module to generate of all stereoisomers and different protonation states and the protein states were optimized by the Protein preparation Wizard module in Maestro (Schrödinger, LLC: New York, NY, 2009). A 30 Å × 30 Å × 30 Å receptor grids centered on Ac-CoA were generated in the Receptor Grid Generation Module. Then docking study was performed using Glide using extra-precision (XP) mode with enhanced planarity of conjugated pi groups, and strain correction terms applied.
6
Structural Analysis of Tubulin-Colchicine Interactions
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The structure of α- and β-tubulin complex with CA-4 (PDB id: 5LYJ) was downloaded from the RCSB PDB protein data bank (https://www.rcsb.org/ ). The protein was prepared by Protein Preparation Wizard module of Schrodinger. Then molecular docking was performed on Maestro 11.5, and PyMOL was used to draw the figures.
7
Optimizing Akt Structure for Docking Studies
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Akt structure was used as per the previously described method [14 (link)]. In brief, crystal structure (PDB # 4ejn) was obtained, and missing loop and side chains were built using Modeller 9.19 and further refined using the protein preparation wizard module of Schrodinger 2018-1. Prior to optimizing the structure with the OPLS-3 forcefield, the bond orders were allocated, and the missing hydrogens were added and applied for docking studies. Ligands were prepared using the LigPrep module from the Schrodinger suite. Glide docking was performed using standard precision mode from the Glide module [15 (link)] of the Schrodinger suite. The grid box was focused on the allosteric pocket of the Akt enzyme as described elsewhere [16 (link)]. LigPrep module was used to prepare the ligands and docked in the generated grid.
8
Protein Structure Optimization Protocol
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The crystal structures of the selected proteins were retrieved from the protein data bank (PDB data base, www.rcsb.org (accessed on 20 September 2022)). The Protein Preparation Wizard module of the Schrödinger suite was used to prepare the proteins. The structures were processed by removing water molecules, adding hydrogen atoms, and filling the chains and loops. Models refinement was performed by energy minimizing the structures employing the OPLS3 force field [32 (link)].
9
Structural Preparation and Docking of Staphylococcus aureus TMPK
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The three-dimensional (3D) crystal structures of Staphylococcus aureus thymidylate kinase (TMPK) were found in the Protein Data Bank database (PDB : ID 4QGG) [14 (link)]. For exact energy measurement, Glide uses a script called “all-atom force field.” Glide additionally reorganizes the missing side chains with steric conflicts, aligning and allocating suitable bond ordering and ionization states. The Protein Preparation Wizard module of the Schrodinger suite was utilized to complete the procedure in its entirety.
The respective pair of receptor fields was represented as a grid with a form and characteristic that consistently allows for more precise ligand pose scoring [15 (link)]. The options in every tab of the receptor network group panel aid in describing the receptor's structure by omitting a few cocrystallized ligands if they are available. Similarly, it helps to set up Glide restrictions by identifying the active site's location and figure as “receptor grids” [16 ].
The respective pair of receptor fields was represented as a grid with a form and characteristic that consistently allows for more precise ligand pose scoring [15 (link)]. The options in every tab of the receptor network group panel aid in describing the receptor's structure by omitting a few cocrystallized ligands if they are available. Similarly, it helps to set up Glide restrictions by identifying the active site's location and figure as “receptor grids” [16 ].
10
Comparative Virtual Screening of IDH1-R132H Inhibitors
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The crystal structures of the IDH1R132H in complex with an inhibitor were downloaded from the PDB database (http://www.rcsb.org ), including 4UMX, 5L57, 5L58, 5LGE, 5SUN, 5SVF, 5TQH, 6ADG, and 6B0Z. For each complex, the Protein Preparation Wizard module in Schrödinger 2015 (Schrödinger, LLC, New York, NY, 2015) was applied to add hydrogen and missing side chains, remove all water molecules, assign protonation states and partial charges through OPLS2005 force field (Jorgensen et al., 1996 (link)), and minimize all heavy atoms until the root-mean-square deviation (RMSD) was reached ≤0.3 Å.
To evaluate the virtual screening capability of different crystal structures, 423 actives were directly extracted from the PubChem database and served as a validation data set (https://pubchem.ncbi.nlm.nih.gov/bioassay/1344832#section=Top ), and their decoys, generated by DUD•E (Mysinger et al., 2012 (link)), were considered as a decoy data set. In total, 23,900 decoys were generated.
To evaluate the virtual screening capability of different crystal structures, 423 actives were directly extracted from the PubChem database and served as a validation data set (
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