Thursday, July 28, 2005

Vega ZZ TOP ROCKS!! Molecular Modeling Tutorial

Whatta sweet program - up there with PYMOL

The integration of ESCHER NG adds Docking capability (the ability to toss a 3D protein file (eg PDB and test its compatability with another protein or a small ligand. To take advantage of this tool you may choose to first apply the MOPAC6 - this will perform quantum mechanic functions on selected regions - by selecting pockets from a 3d server like the Leeds Bioinformatic Pocket Finder You can adjust the selected pocket regions from the resulting pdb file to better understand the docking potentials...

In our example we will look at how the tetrahydrocannabinolic acid synthase [Cannabis sativa (hemp)] molecule you can download the pdb file from the National Institute of Health

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