Molecular Dynamics and Drug Selection

I wanted a selection of drugs in my database, those commonly used such as aspirin , those currently used for myeloma such as lenalidomide, those suggested for the future for myeloma such as JQ1, and those I feel comfortable at trying which have been taken by humanity for centuries and derived from fruits, spices, herbs etc.  For all the drugs we need a PDB file.  You might be able to find it at the RCSB PDB site but you will be able to do so at the  Pubchem site

The example of creating a drug file for aspirin is covered in the  Toenail Example  described in section 4.

Now we have a PDB file and can load it into Autodock Tools.  Here again display, label, atoms  shows the construction.  This program prepares the molecule data to be used in a docking simulation.  As this is a drug it is classed as a "ligand". So ligand, input, choose , the asp we have loaded and charges are added, flexible bonds identified etc , ready for docking.  ligand , output , save as pdbqt gives you the file asp.pdbqt in the location of your choice.

This needs to be done for each and every drug you wish to run test simulations for.

I guess I have several hundred or so now by selection of active molecules from turmeric, green tea, milk thistle, raspberries, apples  etc etc.

If you can get to the same position with curcumin then in Autodock Tools it will look like this.

Curcumin ligand