Question: Binding affinity DB out there?
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gravatar for phosphodiester_bond
3 months ago by
phosphodiester_bond30 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 • 176 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 3 months ago by phosphodiester_bond30

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 3 months ago • written 3 months ago by biostart290
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