Question: Which Downloadable Database Of Pdb Ligand Binding Sites Would You Recommend?
6
gravatar for Jan Kosinski
8.5 years ago by
Jan Kosinski1.6k
Jan Kosinski1.6k wrote:

I am searching for a database of protein ligand binding sites in PDB that

  • is download-able
  • is up to date with PDB (not older that approx. one month)
  • lists residues interacting with that ligand

If I could get interaction types like in PDBe (e.g. http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=3mht&ligandCode3letter=SAH) I would be delighted.

Is anything out there that you could recommend?

pdb interaction • 6.8k views
ADD COMMENTlink modified 6.8 years ago by Adrian0 • written 8.5 years ago by Jan Kosinski1.6k
2

Can't you perform an 'advanced' query and batch download the results?

ADD REPLYlink written 8.5 years ago by Nir London220

Is this not in PDBs FTP site? http://www.pdb.org/pdb/static.do?p=download/ftp/index.html

ADD REPLYlink written 8.5 years ago by Michael Dondrup47k

I think ligand binding site information is not there. I think the binding site data from PDBe is in the PDBe Motif, but I am not sure yet how to download and handle that.

ADD REPLYlink written 8.5 years ago by Jan Kosinski1.6k

Nir, I think I should be able to that using the PDBeMotif web interface, but I simply have no idea how. I queried EBI HELP for that, but I am still waiting for a response.

ADD REPLYlink written 8.5 years ago by Jan Kosinski1.6k

Got the response from EBI HELP. Local installation of PDBeMotif is too difficult and too hardware demanding. And the newest software won't be available. I got some hints about XML queries of PDBeMotif online, but I am not sure yet if it is possible to get all data I need.

ADD REPLYlink written 8.5 years ago by Jan Kosinski1.6k
4
gravatar for Joerg Kurt Wegner
8.5 years ago by
Belgium
Joerg Kurt Wegner230 wrote:

The CREDO database might be a solution, and you might need to check-in with Adrian Schreyer for the update cycles.

ADD COMMENTlink written 8.5 years ago by Joerg Kurt Wegner230
1

CREDO was may favorite, as it has nice python interface, and can be installed easily. I queried Adrian Schreyer a couple of days ago. He says that he will soon do the update (the current version is from July 2010).

ADD REPLYlink written 8.5 years ago by Jan Kosinski1.6k

Cool, that is what I was hoping for!

ADD REPLYlink written 8.5 years ago by Joerg Kurt Wegner230
2
gravatar for Tommy Carstensen
8.5 years ago by
United Kingdom
Tommy Carstensen190 wrote:

Can you use this one? http://www.bigre.ulb.ac.be/Users/benoit/LigASite/

ADD COMMENTlink written 8.5 years ago by Tommy Carstensen190

Thanks, I will try it out. It seems to be updated regularly. The downside is that they use some filtering procedure to filter out small, low contacting ligands (http://www.bigre.ulb.ac.be/Users/benoit/LigASite/index.php?methods). I will look at its content in more detail and post the results here.

ADD REPLYlink written 8.5 years ago by Jan Kosinski1.6k

I have looked at LigASite more carefully and it does not serve my purposes. First, it includes ligand sites only for those proteins for which there is at least one apo- and one holo-structure. Second, it misses some data even if apparently there is both apo- and holo-structure available (e.g. 3kdk).

ADD REPLYlink written 8.5 years ago by Jan Kosinski1.6k
2
gravatar for Khader Shameer
8.4 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Have you tried Catalytic Site Atlas (curated data) ?

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by Khader Shameer18k

To my knowledge, Catalytic Site Atlas is just for catalytic sites, not ligand-binding sites.

ADD REPLYlink written 8.4 years ago by Jan Kosinski1.6k

IMHO, CSA fits the flow's requirement (download-able, is up to date with PDB (not older that approx. one month, lists residues interacting with that ligand).

ADD REPLYlink written 8.4 years ago by Khader Shameer18k

I downloaded the newest CSA dat file from here and the dat file includes only catalytic residues. I am guessing that the only ligand-interacting residues that are listed there will be those that have also been annotated as catalytic.

ADD REPLYlink modified 10 weeks ago by RamRS25k • written 8.4 years ago by Jan Kosinski1.6k
1
gravatar for Vladimir Chupakhin
8.5 years ago by
Toledo, Spain
Vladimir Chupakhin520 wrote:

Try sc-PDB - binding site and proteins are already prepared for docking.

Info from the site: To assist structure-based approaches in drug design, we have processed the PDB to identify binding sites suitable for the docking of a drug-like ligand and we have so created a database called sc-PDB. The sc-PDB database provides separated MOL2 files for the ligand, its binding site and the corresponding protein chain(s). Ions and cofactors at the vicinity of the ligand are included in the protein.

ADD COMMENTlink modified 8.5 years ago • written 8.5 years ago by Vladimir Chupakhin520

Unfortunately, on the website they say that "The database is updated annually", I need sth much up to date.

ADD REPLYlink written 8.5 years ago by Jan Kosinski1.6k

Yep, so at this point is only way - is to prepare it by yourself (also take a look at the preparation of the sc-PDB it might help you).

ADD REPLYlink written 8.5 years ago by Vladimir Chupakhin520
0
gravatar for Jan Kosinski
8.4 years ago by
Jan Kosinski1.6k
Jan Kosinski1.6k wrote:

After getting help from EBI support I got a db of ligand binding sites from PDBeMotif database working, quite up-to-date and local.

I am using it for some time already, and it seems to be cool. It basically lists all bonds to hetatms from PDB, together with distance info, and with annotations on interaction type.

I wrote some quick-and-dirty Python code to download and use this db.

Installation

pip install http://modorama.biocomputing.it/beta_static/src/pdbemotif-0.1.0.tar.gz

It should install pdbemotif Python module, and two scripts should go to your python bin:

download_selected_lig_sites.py
download_all_lig_sites.py

They download data on bonds with protein and hetatms. You can use like this:

python -u path_to_bin/download_all_lig_sites.py /data1/outdir/
python -u path_to_bin/download_selected_lig_sites.py some_pdbcodes.txt /data1/tmp/outdir/

where some some_pdbcodes.txt file lists pdbcodes, one per each line.

Downloading all "sites" takes 3 days. You will get a list of xml files, one per each pdbcode.

Then you can do:

from pdbemotif import BoundMoleculeSite
site_file = open('/data/db/PDBeMotif/3mht.txt')
mol_site = BoundMoleculeSite(site_file.read())
site_file.close()
print mol_site.get_all_binding_resi_for_chain('A')
ADD COMMENTlink written 8.4 years ago by Jan Kosinski1.6k

He already mentioned about PDBeMotif in his question. AFAIK, he is looking for similar/related resources.

ADD REPLYlink written 8.4 years ago by Khader Shameer18k

I think @flow already mentioned about PDBeMotif in his question. AFAIK, he is looking for similar/related resources.

ADD REPLYlink written 8.4 years ago by Khader Shameer18k

Could I still borrow your code? I try the command you pose, but it gave ERROR 404: Not Found. Thanks!

ADD REPLYlink written 6.5 years ago by ajingnk130
0
gravatar for Adrian
6.8 years ago by
Adrian0
Cambridge, United Kingdom
Adrian0 wrote:

The new version of the CREDO database has downloadable data sets of interatomic interactions/structural interaction fingerprints. Currently, there is a comprehensive kinase set but I could create others if there is enough interest.

ADD COMMENTlink written 6.8 years ago by Adrian0

Sounds interesting to me :-)

ADD REPLYlink written 6.8 years ago by Dan500
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