Dear Mohamed, There is a software called CAVER to calculate tunnels in the protein for a given pdb file. ( http://caver.cz/)
It has also a PyMol plugin which you can find from its web site. Burak Sent from my iPhone On 20 Jan 2017, at 18:45, Mohamed Noor <mohamed.n...@staffmail.ul.ie<mailto:mohamed.n...@staffmail.ul.ie>> wrote: Dear all I think this was discussed before on this board but I can't find the relevant thread(s), so apologies. I have a crystal structure on an enzyme with the NAD+ cofactor bound but no substrate, despite trying both co-crystallization and soaking methods and collecting datasets from 20-30 crystals. Is there a way of identifying the approximate path that the substrate takes from the outside into the active site computationally using electrostatics, residue chemistry etc.? Thanks Mohamed
