Computational protocol: Vitexin confers HSF-1 mediated autophagic cell death by activating JNK and ApoL1 in colorectal carcinoma cells

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Protocol publication

[…] 3D structure of HSF-1 (PDB ID: 5D5U) was available at Protein Data Bank (www.rcsb.org) which was retrieved in PDB format. Structure of vitexin (ZINC04245684) was retrieved from ZINC database []. Molecular docking was carried out using Autodock Vina [], which uses pdbqt input files both for ligands as well as protein, to study the nature of interaction of HSF-1 with vitexin, An energy grid box of center grid coordinates used in this study, for Autodock Vina were -10.322 × 4.672 × 23.12 while size used for x, y, z were 44 × 28 × 36, respectively with 1.000Å spacing. Protein residues forming hydrogen and hydrophobic interactions with ligand molecule is further calculated by Ligplot+ software []. […]

Pipeline specifications

Software tools AutoDock Vina, LigPlot+
Application Protein interaction analysis
Organisms Homo sapiens, Homo sapiens/Mus musculus xenograft
Diseases Neoplasms, Colorectal Neoplasms