Autodocktools4

Manufactured by AutoDock

AutoDockTools4 is a software suite designed to facilitate the docking of ligands (small molecules) to receptors (macromolecules). It provides a graphical user interface (GUI) for preparing input files, running AutoDock and AutoDock Vina, and analyzing the results. The core function of AutoDockTools4 is to enable the efficient and accurate prediction of molecular interactions between drug candidates and their target proteins.

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Lab products found in correlation

Vina 1, by AutoDock (2 mentions) Tools, by AutoDock (2 mentions) Discovery studio visualizer, by Dassault Systèmes (2 mentions) Pymol molecular graphics system version 2, by Schrödinger (1 mentions) Pymol molecular graphic system, by DeLano Scientific (1 mentions) Biovia discovery studio 4, by Dassault Systèmes (1 mentions)

26 protocols using autodocktools4

Computational Analysis of Tryptophan Metabolite Binding

Cited 4 times

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The ligand binding affinity of 6 Trpmetabolites, including kynurenine, kynurenic acid, indole-3-carboylate, indole-3-acetate, indole-3-lactate, and indole-3-propionate, were investigated using Autodock Tools 4 and Autodock Vina, and a cryo-EM structure-based computational model of the human AHR PAS B domain.^{27 (link)-30 (link, link, link)} Docking models for each of the 6 Trp-related ligands were obtained from the PubChem database and optimized for docking using Autodock Tools.^{31 (link)} Autodock Vina was run using standard settings, and Grid box parameters generated in Autogrid for a 30 to 60 Å^{3 (link)} docking grid centered on the indirubin binding site, as described previously.^{32 (link)} Docking results were analyzed using Autodock Tools 4 and The PyMOL Molecular Graphics System, Version 2.52 Schrödinger and DeLano, LLC.³³ Active site cavity size was calculated using Caver 3.0.³⁴ AHR docking model quality was validated using an Autodock Vina re-docking analysis with the structural coordinates of indirubin. RMSD re-docking error was calculated using the program LigRMSD.^{35 (link)}

Morgan E.W., Dong F., Annalora A.J., Murray I.A., Wolfe T., Erickson R., Gowda K., Amin S.G., Petersen K.S., Kris-Etherton P.M., Marcus C.B., Walk S.T., Patterson A.D, & Perdew G.H. (2023). Contribution of Circulating Host and Microbial Tryptophan Metabolites Toward Ah Receptor Activation. International Journal of Tryptophan Research : IJTR, 16, 11786469231182510.

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Computational Modeling of AhR Ligand Binding

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The ligand-binding affinity of 3 indolimine analogs, including I-200, I-214, and I-248, was investigated using Autodock Tools 4 and Autodock Vina, and a cryo-EM structure-based computational model of the human AHR PAS B domain [9 (link),20 (link),21 (link),22 (link),23 (link)]. Docking models for the 3 indolimine ligands were built and minimized using PyMOL Molecular Graphics System, Version 2.52 Schrödinger, and LLC and all models were optimized for docking using Autodock Tools [24 ]. Autodock Vina was run using standard settings, using Grid box parameters generated in Autogrid for a 30 Å³ docking grid centered on the indirubin binding site, as described previously [25 (link)]. Docking results were analyzed using Autodock Tools 4 and The PyMOL Molecular Graphics System, Version 2.52. As shown in Supplementary Table S2, AHR docking model quality was validated using an Autodock Vina re-docking analysis with the structural coordinates of indirubin. RMSD re-docking error was calculated using the program LigRMSD, and the AHR PAS B domain cavity size was calculated using Caver Web 1.0 [26 (link),27 (link)].

Patel D., Murray I.A., Dong F., Annalora A.J., Gowda K., Coslo D.M., Krzeminski J., Koo I., Hao F., Amin S.G., Marcus C.B., Patterson A.D, & Perdew G.H. (2023). Induction of AHR Signaling in Response to the Indolimine Class of Microbial Stress Metabolites. Metabolites, 13(9), 985.

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SARS-CoV-2 Main Protease Docking Analyses

Cited 1 time

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A docking experiment was carried out to examine the binding of the renin inhibitors identified by the pharmacophore screening into the active site of the SARS-CoV-2 main protease using Autodock Vina (Oleg and Arthur J, 2010 (link)). The crystal structure of the SARS-CoV-2 main protease (PDB code: 6W63) (Mesecar ) was downloaded from the protein databank (https://www.rcsb.org/). The downloaded structure of the protein was prepared using Autodock tools 4 (J. Westbrook, 2002 (link)), by the deletion of water molecules and assigning of partial charges using Gasteiger charges. Before the docking procedure was performed, validation was carried by the redocking of the co-crystallized ligand. The database of renin inhibitors was also prepared used Autodock tools 4 (J. Westbrook, 2002 (link)), through the addition of Gasteiger charges. The active pocket was defined using a grid box of dimensions 60 X 60 X 60 points centered on the native ligand with a spacing of 0.375 Å. The Lamarckian genetic algorithm was used to carry out a 100 docking runs for each compound using the default Autodock parameters. The results were analyzed and visualized using UCSF Chimera (Morris et al., 2009 (link)).

Refaey R.H., El-Ashrey M.K, & Nissan Y.M. (2020). Repurposing of renin inhibitors as SARS-COV-2 main protease inhibitors: A computational study. Virology, 554, 48-54.

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Molecular Docking for Binding Pocket Identification

Cited 2 times

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To virtually identify the putative binding pocket, molecular docking was carried out through AutoDock Vina (Trott & Olson, 2010 (link)). The receptor PDB file was prepared with AutoDockTools 4 (Morris et al., 2009 (link)) by adding the polar hydrogens and performing the conversion to PDBQT. Likewise, the ligand PDB file was also converted to PDBQT using AutoDockTools 4. The search grid box covered the whole receptor, while the exhaustiveness parameter was set to 10,000. Multiple AutoDock Vina runs with randomized seeds resulted in the same putative binding pocket, indicating an informative prediction (Jaghoori et al., 2016 (link)).

Weiland P., Dempwolff F., Steinchen W., Freibert S., Tian H., Glatter T., Martin R., Thomma B.P., Bange G, & Altegoer F. (2023). Structural and functional analysis of the cerato‐platanin‐like protein Cpl1 suggests diverging functions in smut fungi. Molecular Plant Pathology, 24(7), 768-787.

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Modeling and Docking of Human P-gp

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The human P-gp 3D model was based on the mouse P-gp structure (PDB 4q9h)[34 (link)] which shares 87% of sequence identity. Sequence alignment of the mouse P-gp (UniProtKB P21447) and human P-gp (UniProtKB P08183) was performed with the AlignMe server.[35 (link)] One model was chosen and refined between twenty generated with Modeller 9.19.[36 (link)] For docking experiment, the protein, flexible residues within the drug-binding pocket and ligands were prepared with AutoDockTools 4.[37 (link),38 (link)] Computations were performed by Autodock Vina 1.1.2[39 (link)] to generate 10 poses per molecule with an exhaustiveness parameter of 32. As Autodock Vina does not support Ru atom (Rii = 2.96 Å, epsii = 0.056 kcal.mol⁻¹, vol =12.000 Å³), it was replaced with F (Rii = 3.09 Å, epsii = 0.080 kcal.mol⁻¹, vol = 15.448 Å³) which has the closest energy parameters between all supported atoms, and then replaced back to Ru in resulting poses for visualization purpose.

Côrte-Real L., Karas B., Gírio P., Moreno A., Avecilla F., Marques F., Buckley B.T., Cooper K.R., Doherty C., Falson P., Garcia M.H, & Valente A. (2018). Unprecedented inhibition of P-gp activity by a novel rutheniumcyclopentadienyl compound bearing a bipyridine-biotin ligand. European journal of medicinal chemistry, 163, 853-863.

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Docking of RP-171 and RP-172 to MOR

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One hundred conformers of RP-171 and RP-172 (obtained as described in Section 4.6) were docked into the activated structure of the MOR (PDB accession code: 6DDF [24 (link)], a complex of mu opioid receptor with Gi protein, with DAMGO peptide in the orthosteric binding site) using AutoDock 4.2.6 [25 (link)]. The ligands and the protein were processed in AutoDock Tools 4 [25 (link)]. The ligands’ side chains were allowed to rotate, and the receptor structure was kept rigid. The docking box was set around the position of the DAMGO molecule in the 6DDF structure [24 (link)]. The grids (82 × 78 × 104 points, with 0.375 Å spacing) were calculated with AutoGrid, and the docking was performed using Lamarckian Genetic Algorithm local searches according to the pseudo-Solis and Wets algorithm. Each docking consisted of 100 runs. The results were clustered, and the top scored solutions were visually inspected to examine their conformity to the known literature data on ligand MOR interactions [43 ]. Molecular graphics were prepared in Biovia Discovery Studio Visualizer [44 ].

Wtorek K., Lipiński P.F., Adamska-Bartłomiejczyk A., Piekielna-Ciesielska J., Sukiennik J., Kluczyk A, & Janecka A. (2021). Synthesis, Pharmacological Evaluation, and Computational Studies of Cyclic Opioid Peptidomimetics Containing β3-Lysine. Molecules, 27(1), 151.

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Molecular Docking of Iprodione with MmGSTP1-1

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Molecular docking of iprodione was performed using AutoDock4.2 (version 4.2.6) and AutoDockTools4 [38 (link)]. Ligand-free MmGSTP1-1 and iprodione were used as the receptor and ligand, respectively. The grid was centred at −31, 0, 23 coordinates (with grid sides having 100, 125, and 100 points, spaced at 0.375 Å). AutoDock4.2 was then used for the docking analysis, carrying 100 independent genetic algorithm cycles with a population of 300 individuals. The docked ligand clusters were then further analyzed using PyMOL [39 ]. The refined crystal structure of MmGSTP1-1 resolved in the present study at 1.28 Å resolution was used.

Kupreienko O., Pouliou F., Konstandinidis K., Axarli I., Douni E., Papageorgiou A.C, & Labrou N.E. (2023). Inhibition Analysis and High-Resolution Crystal Structure of Mus musculus Glutathione Transferase P1-1. Biomolecules, 13(4), 613.

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Structural Insights into B. fragilis αGalCer_GT

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The AlphaFold model of B. fragilis αGalCer_GT was obtained from Uniprot A0A380YRQ3. UDP-Gal structure was taken from PDB 5M7D. The complex αGalCer_GT·UDP-Gal was generated by docking with AUTODOCK VINA [42 (link)]. Both the protein and ligand structure were first parametrized with AutoDockTools4 [43 (link)]: polar hydrogens were added, Auto-Dock4.2 atom typing was used, and Gasteiger partial charges were computed. All the rotatable bonds of the ligands were considered free during the docking calculations, whereas the whole protein structure was kept fixed. The docking search space was confined in a box centered in the active site. The exhaustiveness level was set to 24, and 20 binding modes of the ligands were generated. Only low-energy binding poses were considered for analysis. Pictures of the complexes were generated with VMD [44 (link)].

Caballé M., Faijes M, & Planas A. (2022). Characterization of a Glycolipid Synthase Producing α-Galactosylceramide in Bacteroides fragilis. International Journal of Molecular Sciences, 23(22), 13975.

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Docking Assay for Candidate TB506

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To define the coordinates of the active site to launch the docking assay, a structural alignment between the candidate TB506 and the CYP450 prototype (PDB code: 2HPD) (Schuler and Werck-Reichhart, 2003 (link)) was performed by the PyMOL Molecular graphic system (DeLano scientific: San Carlos, CA, United States). Molecular dynamics (MD) calculations were performed by NAMD software using the apo form of the enzyme containing the heme-group (Phillips et al., 2005 (link)). In previous MD calculations, an energy minimization was carried out using standard conditions (10,000 cycles, 1 femtosecond per cycle and a dielectric constant of 80). The MD calculations gave 220 derivative structures from the candidate TB506. Putative substrates were constructed and topologically optimized by ACD/ChemSketch software v1.7 2007 (ACD/Labs: Toronto, ON, Canada). Molecular docking was performed by AutoDockTools 4 (Morris et al., 2009 (link)) providing the coordinates corresponding to the active site of the molecule.

Sanchez-Muñoz R., Perez-Mata E., Almagro L., Cusido R.M., Bonfill M., Palazon J, & Moyano E. (2020). A Novel Hydroxylation Step in the Taxane Biosynthetic Pathway: A New Approach to Paclitaxel Production by Synthetic Biology. Frontiers in Bioengineering and Biotechnology, 8, 410.

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Docking of Compounds to DNA Topoisomerases

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The 13
studied compounds and CP were docked to structures of DNA gyrase (PDB
ID: 5BTC)^{48 (link)} and DNA topoisomerase IV (PDB ID: 3RAD)^{49 (link)} (see Table S2). The docking
procedure is as follows. Ligand structures were generated using the
Automated Topology Builder (ATB version 2.2),^{56 (link)} and topologies were created using the Avogadro^{57 (link)} program. Docking calculations and data analysis were performed
using AutoDock4 (v. 4.2) and AutoDockTools4 programs, respectively.^{58 (link)} 1000 models were generated for each complex
during the docking procedure. Preferred binding modes were selected
based on structural clustering with an rmsd cut-off value of 3 Å.
The central structure of the largest cluster was selected as the final
ligand-docked structure for each complex.

Struga M., Roszkowski P., Bielenica A., Otto-Ślusarczyk D., Stępień K., Stefańska J., Zabost A., Augustynowicz-Kopeć E., Koliński M., Kmiecik S., Myslovska A, & Wrzosek M. (2023). N-Acylated Ciprofloxacin Derivatives: Synthesis and In Vitro Biological Evaluation as Antibacterial and Anticancer Agents. ACS Omega, 8(21), 18663-18684.

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