Question: Setting up an alert for new human PDB ligands
2
gravatar for cdsouthan
5.0 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

Our database team (http://www.guidetopharmacology.org/) would like to set up some kind of allerting triage for the following criteria for humam proteins  a) novel  ligands in an old protein b) old ligands in different proteins b) a protein that gets any ligand for the first time.  There are some additonal filters such chemical property and pocket locations indiciative of specifically bound, lead-like, small-ish, moleculular structure (i.e.pharmcologically-relevant ligands rather than just new hetero atom enties). We'd also want a  frequent-hitters stop list.  For example, we're not that interested in seeing yet more ligands from popular kinases,  BACE1, DPPIV,  FX or thrombin (exept for clinical cpds of course but we can select these anyway).

None of the three WWPDB portals seem to allow such a query off the bat.  In addition we would prefer a transatlantic split in the form of Swiss-Prot IDs for the proteins but PubChem CIDs for the ligands (i.e. rather than gi numbers or UniChem IDs but we could cope with these).  For the record we do check MMDB for novel CIDs and skim the PDBe weekly new entry lists but a specifc allert is obviusly more efficient.   Might a SPARQL query or a KNIME node be an option ?
 

ligands pdb • 1.4k views
ADD COMMENTlink modified 4.4 years ago by conroy20 • written 5.0 years ago by cdsouthan1.8k

This is still a gap for us that we can't really fill with a KNIME node or local PDB copy just now.   Anyone know any other ways forward  (BioMart ?)

ADD REPLYlink written 4.5 years ago by cdsouthan1.8k
2
gravatar for pwrose.ucsd
5.0 years ago by
pwrose.ucsd50
United States
pwrose.ucsd50 wrote:

The folks at Vernalis have written KNIME nodes (http://tech.knime.org/book/vernalis-nodes-for-knime-trusted-extension) that access  RCSB PDB web services (http://www.rcsb.org/pdb/software/rest.do).

Check out this presentation how you might use KNIME to create an alert service for new ligands:

http://www.knime.com/files/006_kuduk_roughley_vernalis.pdf

 

ADD COMMENTlink written 5.0 years ago by pwrose.ucsd50

Useful thanks

ADD REPLYlink written 5.0 years ago by cdsouthan1.8k
1
gravatar for João Rodrigues
5.0 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

I think it's better to have a local copy of the PDB updated in your servers and everytime there is an update, check what is coming in. You should build a database with the information you are looking for (who has ligand, which proteins have which ligands, etc) and then just compare. It's a one-off effort to build this database but then it's only about incremental updates and checks, which could make it very manageable. You can even get rid of the structural data once you populate the DB to save space.

p.s. I'm not very familiar with KNIME nodes or SPARQL queries, so apologies for the general answer..

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by João Rodrigues2.5k

Thanks, we'll cogitate on this

ADD REPLYlink written 5.0 years ago by cdsouthan1.8k
1
gravatar for conroy
4.4 years ago by
conroy20
United Kingdom
conroy20 wrote:

This URL http://www.ebi.ac.uk/pdbe/entry/search/index?document_type:latest_chemistry&view=compounds&organism_scientific_name:%22Homo%20sapiens%22 will display the ligands which are new to the PDB in the current week which are bound to human proteins

ADD COMMENTlink written 4.4 years ago by conroy20

Ta, it works - super

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by cdsouthan1.8k
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