Computational protocol: A Combinatorial approach: To design inhibitory molecules on Hemagglutinin protein of H1N1 virus (Swine Flu)

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[…] The structure of HA protein of swine flu H1N1 along with a ligands and water molecules were downloaded from RCSB Protein Data Bank (PDB ID: 1RUY in website http://www.rcsb.org/pdb) (). 1RUY protein 3D molecules and anti drug molecule thiazolide were used for designing new inhibitor molecules. We took thiazolide as seed molecule and chemical structure was drawn using software ACD ChemSketch into as a mol file ().Then mol file was converted into .sdf file by using Open Babel software. Combinatorial library designed by using known inhibitor thiazolide with the help of random library generation process []. For the high quality molecular diversity library generation, ILib diverse software was used []. This program was also designed for obtaining compound libraries with an optimal molecular diversity [] in which molecules were filtered by using the Lipinski's rule of 5 which is the most approved filter for discernment between drug-like and non drug-like molecules []. For the conversion of 2D SDFile format into 3D SDFile format Corina software was used. It automatically generates three-dimensional atomic coordinates from the structure of a molecule and expresses it as a connection table or linear code, for large databases. The generated 3D library was used for virtual screening for finding new inhibitor for HA []. [...] Molegro Virtual Docker (MVD) is software for studying and predicting ligands interaction towards macromolecules. The docking performed by using flexible docking method of MVD []. Docking was performed for designed combinatorial library molecules on binding site of 1RUY protein. […]

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