Question: Binding affinity DB out there?
0
gravatar for phosphodiester_bond
21 months ago by
phosphodiester_bond40 wrote:

I know this is a long shot, but...

Say you have a compound (could be a drug, but not necessarily), and a particular protein of interest. What is currently the simplest way to obtain some quantitative measure of binding affinity between them? Is there an up-to-date database where ligand/receptor affinity is curated? I found several projects online, most old and focused on protein-protein affinity.

I'm not interested in just documented strong affinity between chemical A and protein X (I can get that from the Uniprot entry for the protein in question), but also interested in poor affinity between chemical B and protein Y. Of course, a lack of a documented binding affinity doesn't necessarily imply there's poor affinity between B and Y. So, I was looking for either a curated resource that is somewhat up to date, or one that I could use to provide a chemical (SMILES, CAS nr, DrugBank ID, etc) and a protein (Uniprot ID, etc) and calculate a metric of affinity based on the chemical/conformational properties of each.

affinity curation binding • 456 views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 21 months ago by phosphodiester_bond40

What kind of chemicals?

For antibodies you may try this: http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/Welcome.php

For protein-ligand this: http://nldb.hgc.jp/nldb/top

For new small compounds it may be easier to do your own docking simulation though

ADD REPLYlink modified 20 months ago • written 20 months ago by biostart350
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 915 users visited in the last hour