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AutoDock Tools version 1.5.6

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AutoDock Tools version 1.5.6 is a molecular docking software that allows users to predict the interaction between a small molecule and a target protein. The software provides a graphical user interface (GUI) to set up, run, and analyze molecular docking experiments. It includes tools for preparing input files, visualizing the results, and analyzing the predicted binding modes.

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26 protocols using AutoDock Tools version 1.5.6

The X-ray crystal structures of P13K alpha (PDB ID: 6PYS) and P13K gamma (PDB ID: 5JHB) were downloaded from the Protein Data Bank and prepared using a standard protocol. The structures were loaded into Biovia Discovery Studio 2021 Client. Heteroatoms such as water are removed. The binding site attributes were determined based on the location of the co-crystalized ligand. The co-crystallized ligands (P5J and 6K5) for each structure were removed, charges were then added, and the structures were then saved as prepared protein. The prepared structures were then loaded into AutoDock Tools version 1.5.7 [52 (link)] and saved in pdbqt format.
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The 3D structures of active ingredients, such as glabrone, p-hydroxybenzaldehyde, ginkgolic acid and dihydroartemisinic acid, were obtained from the PubChem database and the Protein Data Bank (https://www.rcsb.org/). OpenBabel was used for format conversion. AutoDock Tools version 1.5.7 was used to perform molecular docking. Discovery Studio 2021 was used to visually analyse the docking results (Yang et al., 2022b (link)).
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The crystal structure of miransertib (ARQ092) in complex with the Akt-1 [40 (link)] was retrieved from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (PDB code: 5KCV) [41 (link)]. All water molecules and co-crystal ligand were deleted with the UCSF ChimeraX [42 (link)]. AutoDockTools version 1.5.7 [43 (link)] was used to repair missing atoms and add polar hydrogen atoms. The structure of OBA-RT was constructed utilizing MarvinSketch and optimized with the Gaussian 09 program [44 ] using density functional theory (DFT) with a B3LYP/6-31G (d,p) basis set. Autodock Vina [45 (link)] was performed to investigate an interaction between OBA-RT and the allosteric pocket of Akt-1 using default parameters. A grid box was set with the center of the co-crystal ligand (PDB code: 5KCV). The grid size was set to 20 × 20 × 20 Å with a spacing of 1 Å. Furthermore, visualization of binding interaction patterns was carried out by UCSF ChimeraX.
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We evaluate the interaction between COX-2 and curcuminoid polyphenols found in CL, as curcumin, demethoxycurcumin and bisdemethoxycurcumin, via molecular docking. To this end, the crystal structure of COX-2 (PDB code 3LN1) was retrieved from the Protein Data Bank (Berman et al., 2000 (link)), whereas the 3D structure of curcumin, demethoxycurcumin and bisdemethoxycurcumin, etodolac, rofecoxib, valdecoxib, lumiracoxib, celecoxib, etoricoxib and meloxicam were retrieved in SDF file format from the PubChem database at NCBI (Pubchem CID: 969516, 5469424, 5315472, 3308, 5090, 11960, 151166, 2662, 123619, 54677470, respectively). Etodolac, rofecoxib, valdecoxib, celecoxib, etoricoxib, meloxicam and nabumetone were used as reference compounds to compare their affinity to COX-2 with that of curcuminoid polyphenols because they are COX-2 selective non-steroidal anti-inflammatory drugs (NSAIDs) (Chen et al., 2008 ). Here we performed rigid docking taking whole receptor in order to identify the potential binding site and associated binding energy. Both ligands and protein were prepared using AutoDock Tools version 1.5.6 (ADT), as previously described (Guzmán et al., 2020 (link)). Finally, graphic analysis of molecular docking studies were performed using VMD (Humphrey et al., 1996 (link)).
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The 3D crystal protein-structures of SARS-CoV-2 3CLpro (PDB ID: 6LU7) (Hall and Ji, 2020 (link)), SARS-CoV-2 spike protein-ACE-2 receptor-binding domain (RBD) (PDB ID: 6M17) (Wu et al., 2020 (link)), and human ACE2 (PDB ID: 1R4L) (Joshi et al., 2020 (link)) were obtained from the RCSB PDB database (http://www.rcsb.org/pdb). The 3D crystal structures of SARS-CoV-2 RdRp generated through homology modeling using ICM 3.7.3 modeling software was gifted by Prof. Hua Li, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (Wu et al., 2020 (link)). The energy minimization of targeted protein structures was performed using the YASARA server. The protein preparation was done with AutoDock Tools Version 1.5.6.
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The 3D crystal structure of SARS-CoV-2 main protease, Mpro was selected from RCSB PDB [52 (link)]. The protein with PDB code 7D1M was selected for the task where Mpro was bound with GC376. The protein structure inhibitors were separated by releasing the atomic coordinates, using UCSF Chimera to get Mpro protein in the free form [53 (link)]. AutoDock Tools version 1.5.6 was used to add all the missing hydrogens, designation of partial charges, calculating Gasteiger charges to the macromolecule.
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Molecular docking studies were performed using AutoDock 4.2 and AutoDock Tools version 1.5.6 (ADT). The 3D structure of TcPMCA1 (GenBank No. KP455490), and its binding pocket were obtained from the I-TASSER server (Available online: http://zhanglab.ccmb.med.umich.edu/I-TASSER/), then water molecules were removed, polar hydrogen atoms were added, Compute Gasteiger charges were added, and AD 4 type atoms were assigned [41 (link)]. The 3D structure of ligands were constructed and their energy minimization were performed using ChemOffice 2004. Following by the structural optimization, all ligands were prepared for docking by merging non-polar hydrogen atoms, detecting rotatable bonds and adding gasteiger charges [41 (link)]. The grid box size of 60 × 60 ×60 Å was generated and allocated to center of binding cavity using x, y and z coordinates of 102.273, 100.115, and 118.080 for intend searching modality. Other parameters were set as the default. The Lamarckian genetic algorithmwas applied to calculate the possible conformation of the ligand molecule and macromolecule. Finally, the docking results were analyzed using the free version of Discovery Studio Visualizer 4.5 (Accelrys Software Inc., San Diego, CA, USA) [58 (link)].
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8

Molecular Docking of Usnic Acid with S. mutans Proteins

Crystal structures of S. mutans response regulator VicR domain (PDB ID: 5ZA3) and GtfC (PDB ID: 3AIC) was obtained from the PDB database. Chemical structure of usnic acid was retrieved from PubChem database (PubChem CID: 5646). Protein was prepared using the AutoDock Tools Version 1.5.6 and the molecular docking was performed through AutoDock Vina software56 (link). Protein–ligand interactions were analysed and structural figures were prepared using Maestro 10 (Schrödinger) software.
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9

Molecular Docking of Compounds with TcSir2rp1 and Human SIRT2

The 3.5 Å crystal structure of TcSir2rp1 was used for docking of compounds 9, 1a and 1b. Additionally, crystal structures of human SIRT2 were downloaded from the RCSB Protein Data Bank [59 (link)] (3zgo, [60 (link)]; 4rmj, [61 (link)]; 4rmg, [62 (link)]. AutoDock Tools version 1.5.6 was used to prepare the protein model for docking [62 (link)]. We used the protein models with and without ligands (an acetylated fragment of p53 for TcSir2, ADP and nicotinamide for 4rmj, NAD+ and SirtReal for 4rmg). Water molecules were removed, polar hydrogens added, charges for the protein calculated and a pdbqt file for each protein model produced. Coordinates for the docking search grid were also determined. Ligands were prepared for docking by drawing their structures in Chem3D, optimising mm2, and writing the structures to pdb files. AutoDock Tools were then used to produce a PDBQT file for each ligand [63 ]. Docking was performed with AutoDock Vina [64 ]. PyMOL (version 1.5.0.4, [65 ]) was used to visualize the molecular models.
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Molecular docking was performed to investigate the binding mode of SSC to HSA by means of Autodock Vina software (version 1.1.2). The three-dimensional (3D) coordinate of the HSA (PDB ID: 2XVU) was downloaded from the Protein Data Bank (http://www.rcsb.org/pdb) [48 ]. The Auto Dock Tools version 1.5.6 software (http://mgltools.scripps.edu) was employed to generate the docking input files. Ligand structure was prepared for docking by merging non-polar hydrogen atoms and defining rotatable bonds. In order to increase the docking accuracy, the value of exhaustiveness was set to 20. For Vina docking, the default parameters were used as described in the Autodock Vina manual unless otherwise specified. The top ranked pose as judged by the Vina docking score was subject to visually analysis by using PyMOL 1.7 software (http://www.pymol.org/).
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