Question: Database Or Repository Containing All Protein Structures From Pdb In Docking Ready Format (Pdb, Mol2)
1
gravatar for Flow
6.1 years ago by
Flow1.5k
Flow1.5k wrote:

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.

pdb protein • 3.9k views
ADD COMMENTlink modified 6.1 years ago by Vladimir Chupakhin520 • written 6.1 years ago by Flow1.5k
2
gravatar for wdiwdi
6.1 years ago by
wdiwdi380
Germany
wdiwdi380 wrote:

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

ADD COMMENTlink written 6.1 years ago by wdiwdi380

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..)

ADD REPLYlink written 6.1 years ago by João Rodrigues2.5k
0
gravatar for Vladimir Chupakhin
6.1 years ago by
Toledo, Spain
Vladimir Chupakhin520 wrote:

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.

ADD COMMENTlink written 6.1 years ago by Vladimir Chupakhin520

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

ADD REPLYlink written 6.1 years ago by Flow1.5k
1

Google the name :)

ADD REPLYlink written 6.1 years ago by João Rodrigues2.5k

Done, now it works (server was down before)

ADD REPLYlink written 6.1 years ago by Flow1.5k
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