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Tools ver 1.5.6

Manufactured by AutoDock

AutoDock Tools (ver. 1.5.6) is a software package that provides a graphical user interface for the AutoDock molecular docking program. The core function of AutoDock Tools is to facilitate the preparation of input files and the analysis of docking results for molecular docking simulations.

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Lab products found in correlation

3 protocols using tools ver 1.5.6

1

Identification of Obesity-Related Targets for EQST

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The two-dimensional molecular structure of EQST (Fig. 1A) was downloaded from PubChem (https://pubchem.ncbi.nlm.nih.gov, PubChem CID: 54684703), and minimized in Discovery Studio ver. 4.5. The RCSB Protein Data Bank (https://www.rcsb.org) is used to retrieve the released three-dimensional structures of human proteins. DS 4.5 has been used to hydrogenate proteins, remove water and the ligand molecules. AutoDockTools ver. 1.5.6 was used to convert EQST and protein molecules into “pdbqt” format, and finally vina was been used for molecular docking. Generally, if the affinity value is less than −6 kcal/mol, the small molecule can be considered as a potential ligand of the receptor35 (link). The receptors with a docking score less than −9 kcal/mol are considered as the potential target proteins of EQST. Obesity-related proteins with a relevance score higher than 10 were retrieved from the GeneCards database (https://www.genecards.org/) by searching the term of “obesity”. The two sets of the proteins were subjected to Venn analysis using the Venny 2.1.0 online tool to identify candidate obesity-related targets of EQST.
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2

Molecular Docking of G-Quadruplex Ligands

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Molecular docking study was performed using the solution structure of anti-parallel human telomeric DNA G-quadruplex (PDBID: 2mb3) [45] . The first two thymine residues at the 5' end and the last residue adenine at the 3' end were deleted to produce 21-mer G-quadruplex. The 3D structures of the small molecules were generated with DS viewer 3.5. Autodock Tools (ver. 1.5.6) was used to convert the structure files to pdbqt format. [54] Docking was performed using the AUTODOCK vina program. [55] The dimensions of the active site box were chosen to be large enough to encompass the entire G-quadruplex structures. An exhaustiveness of 20 was used and other parameters were left as default.
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3

Molecular Docking of G-Quadruplex DNA

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Molecular docking study was performed using the solution structure of anti-parallel human telomeric DNA G-quadruplex (PDB ID: 2mb3) [55] . The first two thymine residues at the 5'-end and the last residue adenine at the 3'-end were deleted to produce 21-mer G-quadruplex. The NMR structure of duplex DNA 5'-d(CGCTAGCG)-3' in complex with homodimeric thiazole orange dye (TO) (PDB ID: 108D) was used for the modeling of intercalation interaction. [56] The 3D structures of the small molecules were generated with DS viewer 3.5. Autodock Tools (ver. 1.5.6) was used to convert the structure files to pdbqt format. [57] Docking was performed using the AUTODOCK vina program. [58] The dimensions of the active site box were chosen to be large enough to encompass the entire Gquadruplex structures. An exhaustiveness of 100 was used and other parameters were left as default.
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