Question: Binding affinity DB out there?
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:

For protein-ligand this:

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
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