As we know docking software like molegro, Autodock, Autovina have ligand specification of 14 atoms with 50-60 bonds and schrodinger has 16 atoms with approx 100 bonds. So is there open available software for docking with Incorporation of whole protein as a ligand No compulsion of no. of Atoms.
Because I need to incorporate whole proteins as ligands and I cannot only take the active site of the protein.
Sergey Shityakov i have Hex but not well versed with the process. How i can do it. does we need to make special file format.
Hi,
are you trying to perform protein-protein docking? If so, have look to HADDOCK http://www.nmr.chem.uu.nl/haddock/
There are several macromolecular docking software such as Hex, Patchdock ...
You can try patchdock for the docking step followed by using fiberdock to refine the resulting complexes
Glide actually supports 100 rotatable bonds in the novel release of Schrodinger suite 2015
The Hex docking engine uses the SPF representation, and its main weakness is that it only encodes shapes sharply up to about 30 Angstroms from the molecular origin (rotation center), and the correlations are only meaningful up to about 60 A between a pair of molecular origins.
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