Question: R Or Python Package For Reverse/Inverse Docking ( To Use A Ligand To Fish All The Targets)
0
gravatar for Pradeep
6.6 years ago by
Pradeep70
south korea
Pradeep70 wrote:

Please suggest tools/programming libraries/API for inverse/reverse docking. Tool should support target-fishing at genome scale either by programming ( python / R) or by batch mode feature.

docking • 3.4k views
ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Pradeep70
2

OK, a simple question: Have you even _tried_ searching PubMed before posting here? Your question does not indicate at all what you have tried.

ADD REPLYlink written 6.6 years ago by David Westergaard1.4k

another relevant question: Do author know what inverse docking is?

ADD REPLYlink written 6.6 years ago by Vladimir Chupakhin520

Chup4: I am new to this kind of work. I picked up inverse /reverse docking term looking at a tool INVDOCK ( http://wenku.baidu.com/view/66056ce9aeaad1f346933fd8 ) and other similar online tools which does drug-target fishing. I may be wrong calling it that way -- if so Chup4, please feel to correct me. Thank you. NOTE: unfortunately INVDOck is not available for download from author's site.

ADD REPLYlink written 6.6 years ago by Pradeep70

Yes David, I have meticulously searched PubMed, Google Scholar and even Google. I am not convinced with my finding that there may be no tools.

ADD REPLYlink written 6.6 years ago by Pradeep70

You mean, using a known ligand to see which proteins it binds to? You can do it in structural databases (advanced search in RCSB PDB), but other than that... it's very complicated. If I understood you correctly.

ADD REPLYlink written 6.6 years ago by João Rodrigues2.5k

João Rodrigues:

ligand has no known targets. So, has to bee either by reverse docking it with all (most likely a list from proteomics/microarray study) proteins in the uniprot database.

ADD REPLYlink written 6.6 years ago by Pradeep70

My suggestion would be to try and make a scheme of the ligand, identify functional groups, and search for structures containing drugs with similar groups. You can identify similar drugs very easily with existing tools (look for drug similarity, tanimoto scores, etc, you'll find plenty of resources) and then find the best matching in a database like the PDB. A little scripting can help.

ADD REPLYlink written 6.6 years ago by João Rodrigues2.5k
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