Molecular Docking of Bioactive Compounds

The crystal structure of TLR4 came from the Protein Data Bank (PDB code: 2Z66). The ligands and water molecules were removed from the crystal structure via Pymol (

https://pymol.org/2/

). The structure of bergenin, chlorogenic acid, and ammonium glycyrrhizate (ammonium removed) was obtained from PubChem database (

https://pubchem.ncbi.nlm.nih.gov/

) and hydrogen atoms were added by using AutoDock Vina software. The rigid target-site docking procedures were performed using AutoDock Vina software with a genetic algorithm.15 (link) Hydrogen bonds and bond lengthanalysis and visualization were performed using Pymol.

Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link: Access Free Full Text.

Yan L.S., Cui S., Cheng B.C., Yin X.B., Wang Y.W., Qiu X.Y., Nima C.R., Zhang Y, & Zhang S.F. (2023). Sichen Formula Ameliorates Lipopolysaccharide-Induced Acute Lung Injury via Blocking the TLR4 Signaling Pathways. Drug Design, Development and Therapy, 17, 297-312.

Publication 2023

AutoDock Vina software

Ammonium Autodock Bergenin Chlorogenic acid Hydrogen Hydrogen bonds Ligands Rigid

Corresponding Organization :

Other organizations : Beijing University of Chinese Medicine, Hong Kong Polytechnic University, Tibetan Traditional Medical College

Top 5 similar protocols

Variable analysis

independent variables

Bergenin
Chlorogenic acid
Ammonium glycyrrhizate (ammonium removed)

dependent variables

Hydrogen bonds
Bond length

control variables

TLR4 crystal structure (PDB code: 2Z66)
Ligands and water molecules removed from the crystal structure via Pymol
Hydrogen atoms added to the ligand structures using AutoDock Vina software
Rigid target-site docking procedures performed using AutoDock Vina software with a genetic algorithm

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

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?

Revolutionizing how scientists
search and build protocols!