Database Or Repository Containing All Protein Structures From Pdb In Docking Ready Format (Pdb, Mol2)

Question

[Flow]

I have some ligand structures and I would like to which proteins it could interact to. For that I would like to use docking, and use all protein structures from PDB. Therefore I wonder whether a database or repository containing all 3D protein structures in docking ready format (pdb, mol2) exists.

Answer 1

[wdiwdi]

Maybe I am missing something, but why are you not simply using the official PDB database www.rcsb.org/pdb to get PDB files?

[João Rodrigues]

The problem with structures in the PDB is that they contain ligands, solvent molecules, breaks in the polypeptide chain, and numerous numerous other problems that make docking programs crash unexpectedly. Curating a benchmark is a pain.. But anyway, I would indeed do this manually because it depends on what proteins your ligand is targetting (you should have an idea..)

Answer 2

[Vladimir Chupakhin]

try sc-pdb, is not full and updated on yearly basis, but ready to dock. preparing the pdb's is a really REALLY tremendous task.

[Flow]

I clicked on the link, but it says "not found"!

[João Rodrigues]

Google the name :)

[Flow]

Done, now it works (server was down before)