The largest database of trusted experimental protocols

Tools 4

Manufactured by AutoDock

AutoDock Tools 4.2 is a molecular docking software that provides a platform for predicting the binding of small molecules to target proteins. It enables the user to prepare input files, run docking simulations, and analyze the results. The software is designed to be user-friendly and provides a graphical user interface for ease of use. AutoDock Tools 4.2 is widely used in the field of computational chemistry and drug discovery.

Automatically generated - may contain errors

43 protocols using tools 4

1

Molecular Docking of Antibiotic Compounds

Check if the same lab product or an alternative is used in the 5 most similar protocols
The structures of the compounds were converted to 3D structures with added polar hydrogen bonds using Open Babel [32 (link)]. The structure of AAC(6’)-Ib complexed with kanamycin C and AcetylCoA [27 (link)] was obtained from the protein data bank (PDB 1V0C). The AAC(6′)-Ib protein with kanamycin C removed and the compounds were prepared in the pdqt format using AutoDockTools 4.2 [33 (link)]. A cavity in the kanamycin C binding region of the protein was selected as the target site for virtual screening. Vina from AutoDockTools 4.2 [33 (link)] was used to perform docking and screening. The docking scores were sorted and ranked based on their predicted binding energies. LigPlot+ [34 (link)] was used to generate a 2D ligand–protein interaction map. PyMol 2.3 (Schrodinger) was used for visualization and rendering.
+ Open protocol
+ Expand
2

Molecular Docking of VCP Inhibitors

Check if the same lab product or an alternative is used in the 5 most similar protocols
All molecular docking experiments were carried out with AutoDock Vina.29 (link) The structure of VCP was acquired from the protein data bank (PDB code 5FTK), and modified by removing the bound ADP and solvent molecules, and converted to a hexameric form for CB-5083 and NMS-873.2 (link) Auto-DockTools 4.2 was utilized to add polar hydrogens and Gasteiger charges and to position a 30×30×30 Å3 search box that included both E470 and the active site.33 (link) Structure coordinates of compounds of interest were built using Phenix and then converted to a.pdbqt format with Auto-DockTools 4.2, allowing full ligand flexibility.34 (link) Default Autodock Vina settings were utilized for the analysis of binding modes, except that exhaustiveness was raised to 100. Measurements and figures were made in PyMol.35
+ Open protocol
+ Expand
3

Computational Analysis of Ligand-Protein Interactions

Check if the same lab product or an alternative is used in the 5 most similar protocols
The elastase receptor 1qnj was downloaded from RCSB15 (link) and ligands were removed from the protein file employing Pymol 2.3. Then, AutoDock Tools 4.2 was used to remove water molecules, add hydrogens, assign AD4 type to all atoms, compute Gasteiger charges and save protein files both in pdb and pdbqt formats16 (link).
The α and β-acid and prenylflavonoid molecules 6-prenynlaringenin, adhumulone, cohumulone, cis-isohumulone, cis-isocohumulone, R-humulone, 8-prenylnaringenin, 6-geranylnaringenin, desmethylxanthohumol, xanthohumol, trans-isocohumulone, trans-isohumulone, isocohumulone, isoadhumulone, lupulone, cis-tetrahydroisocohumulone, cis-tetrahydroisohumulone, isoxanthohumol, trans-tetrahydroisohumulone, trans-isocohumulone, trans-tetrahydroisocohumulone, and colupulone were downloaded from Chemspider (http://www.chemspider.com) or Pubchem (http://www.pubchem.ncbi.nlm.nih.gov) in mol format and were converted to mol2, pdbqt and pdb using Pymol 2.3, AutoDock Tools 4.2 and Openbabel GUI 2.4.1.
+ Open protocol
+ Expand
4

SARS-CoV-2 Viral RdRp Structure Preparation

Check if the same lab product or an alternative is used in the 5 most similar protocols
The Viral RdRp of SARS-CoV-2 (PDB: 7BTF) was obtained from Protein Data Bank (PDB, https://www.rcsb.org/) and processed in Biovia Discovery Studio 2021 (Discovery Studio Visualizer, 2020 ) and AutoDock tools 4.2 (Rizvi et al., 2003 ). The binding site (Coordinates: x = 127.0598, y = 124.6167, and z = 128.7631; Size: x = 14, y = 14, and z = 14) of the protein were defined in Biovia Discovery Studio 2021. Followed by, removing the heteroatom and water molecules from the protein. Then, the polar hydrogens, Kollman charge, missing atom, and Autodock4 atom types were added into the pre-processed protein by AutoDock tools 4.2. After processing, the proteins were submitted to UCLA-DOE-LAB SAVES v6.0 (saves.mbi.ucla.edu) and Ramachandran plot server (Anderson et al., 2005 ).
+ Open protocol
+ Expand
5

Extraction and Preparation of FDA-Approved Drugs

Check if the same lab product or an alternative is used in the 5 most similar protocols
2100 FDA-approved drugs were extracted from the PubChem database. Inappropriate, organic polymers and inorganic compounds were removed manually. Then the structures of the ligands were prepared by AutoDock Tools 4.2. The SDF format was converted to PDB format using OpenBabel (version 2.4.1). Nonpolar hydrogen bonds were integrated, Gasteiger-Marsili charges were assigned, atoms were set with AutoDock atom types, and rotatable bonds were assigned and saved in pdbqt format using AutoDock Tools 4.2.
+ Open protocol
+ Expand
6

Structural Preparation of MAO-A Enzyme

Check if the same lab product or an alternative is used in the 5 most similar protocols
The crystallographic structure of MAO-A enzyme (pdb: 2Z5X) in complex with harmine was downloaded from the Protein Data Bank RSCB PDB. The raw crystal structure of MAO-A was prepared with AutoDock Tools 4.2 where all water molecules, ligands and co-factors were removed, while Kollman united-atom partial charges for neutralization of the enzyme were added, as well non-polar hydrogens were merged. All hydrogen atoms of MAO-A were further optimized by using the MolProbity application to generate a correct hydrogen bond network. This enzyme structure was saved in pdbqt format in AutoDock Tools 4.2.
+ Open protocol
+ Expand
7

Molecular Docking with AutoDock Tools

Check if the same lab product or an alternative is used in the 5 most similar protocols
Molecular docking was performed using AutoDock Tools 4.2.1 version88 (link). The polar hydrogen was added to the receptor (proteins) followed by addition of Kollman charges and computing Gasteiger charges. The torsions were calculated for respective ligands and both receptor and ligand files were saved as .pdbqt format. The grid optimization was performed using AutoGrid programme and the grid box was centered such that it covers all identified active pocket amino acid residues. Docking was carried out using AutoDock programme and ten different conformations were generated with respect to their binding energies. The energy values in AutoDock are calculated on basis of various intermolecular bonds such as- hydrogen bond, desolvation energy, van der Waals, and electrostatic energy, internal energy of ligand, and torsional free energy. Amongst these, the desolvation and van der Waals energy together forms the binding energy; the hydrogen bond and van der Waals energy forms the docking energy and the strength of binding of ligand to the receptor is determined by electrostatic interactions. Complexes having lowest binding energy were considered as the best receptor-ligand structure and were chosen for post docking analysis. The results were visualized using Discovery Studio Visualizer and MOE (Molecular Operating Environment) softwares.
+ Open protocol
+ Expand
8

Molecular Docking Analysis for Receptor-Ligand Interactions

Check if the same lab product or an alternative is used in the 5 most similar protocols
Molecular docking was performed using AutoDock Tools 4.2.1 version [88]. The polar hydrogen was added to the receptor (proteins) followed by addition of Kollman charges and computing Gasteiger charges. The torsions were calculated for respective ligands and both receptor and ligand les were saved as .pdbqt format. The grid optimization was performed using AutoGrid programme and the grid box was centered such that it covers all identi ed active pocket amino acid residues. Docking was carried out using AutoDock programme and ten different conformations were generated with respect to their binding energies. The energy values in AutoDock are calculated on basis of various intermolecular bonds such as-hydrogen bond, desolvation energy, van der Waals, and electrostatic energy, internal energy of ligand, and torsional free energy. Amongst these, the desolvation and van der Waals energy together forms the binding energy; the hydrogen bond and van der Waals energy forms the docking energy and the strength of binding of ligand to the receptor is determined by electrostatic interactions. Complexes having lowest binding energy were considered as the best receptor-ligand structure and were chosen for post docking analysis. The results were visualized using Discovery Studio Visualizer and MOE (Molecular Operating Environment).
+ Open protocol
+ Expand
9

Molecular Docking of Compounds using Avogadro and AutoDock

Check if the same lab product or an alternative is used in the 5 most similar protocols
The 3D structures of titled compounds were drawn, and energy of each compound was minimized and saved in the pdb format by using Avogadro [28 (link)]. Subsequently, AutoDock Tools 4.2 [29 (link)] was used to open the pdb files, and torque adjustment was made by detecting roots and adjusting as desired. Then, the files were saved in the pdbqt format. Meantime, the structure data format (SDF) structure of the control, lopinavir (CID: 92727), was downloaded from the PubChem database (www.pubchem.ncbi.nlm.nih.gov). The structure data file (SDF) format was subjected to the energy minimization process using MMFF94 (Merck Molecular Force Field 94) force field algorithm [30 (link)], the minimized structure was converted into PDBQT format using PyRx before performing molecular docking analysis.
+ Open protocol
+ Expand
10

Structural Analysis of Human ACE2 for Docking

Check if the same lab product or an alternative is used in the 5 most similar protocols
The structure of human ACE2 was retrieved from protein data bank (www.rcsb.org) with PDB ID: 6VW1 which is a newly released crystal structure of human ACE2 that is complexed with the 2019-nCoV chimeric receptor-binding domain. Protein was prepared for docking using AutoDock Tools 4.2. The ligands, ions, and all the water molecules were removed from the PDB file. Charges and missing hydrogen atoms were added to the human ACE2 receptor in the AutoDock Tools environment and were saved in pdbqt format to be used in the following steps.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!