Reading an account of the session at the ACS on application of computational methods to FBDD, reminded me that it would be a good time to raise awareness of networking groups in this area. Both this blog and Practical Fragments allow readers to comment on posts although this tends not to happen with the frequency that it does at In the Pipeline, probably reflecting the huge readership, frequent updating and diverse content of what I consider to be the best drug discovery blog by a long way.
People interested in FBDD may already belong to a number of relevant LinkedIn groups. The groups offer some advantages over blogs for getting discussions going in that anyone can start a discussion and group members get alerted by email whenever somebody makes a new comment. I’ll list some of these below in case there are some that you’ve not yet heard about.
Fragment Based Drug Discovery (This group is linked by both FBDD blogs)
Label Free Assay Technology Group (It is the assay that makes FBDD possible. The weaker the binding that you can measure reliably, the more powerful your assay)
Structural Biology (X-ray Crystallography, NMR Spectroscopy, Electron Microscopy) (Generally you’re going to need crystal structures to take fragment hits forward)
Job opportunities in Computational Chemistry and Biology, Xray Crystallography, Fragment Based DD
Recently, I submitted the same item for discussion at a number of LinkedIn groups. I invited group members to share their views on the most appropriate technologies for detecting fragment binding. I learned about some new ways to configure SPR experiments and the use of Tm-shift assays. Most of the discussion was in the Structural Biology group (see discussion) although there was helpful input from the relatively new Label Free Assay Technology Group (see discussion) so thank you to all the participants. It was also great to see a couple of familiar faces from my days in Big Pharma, including a co-author from an article that a number of us wrote back in 2007
4 comments:
Hey!
Thank you very much for your comment on my blog! I'm glad you liked the pictures of Agra, it's a beautiful place...:)
Wow, Melbourne? I'd love to visit Australia...!
Thanks again for your comment. And enjoy your world trip!:)
Take care!
Vandana
Glad that you found the blog. As you can see it's technical and lacks the nice photos of Agra that your blog has. However, I may upload a couple of photos because I had a look around the Australian synchrotron yesterday.
Hello, I am a researcher in computational protein design, and don't know much about FDBB, but find it quite intriguing! I came across your blog during a google search. I am interested in the inverse problem of FDBB i.e. given a small molecule ligand, design (or redesign) a protein to bind to it. I'd like to create a dictionary of ligand fragment-protein sidechain interaction pairs from the PDB. I was thinking of using techniques from FDBB to break a given ligand into its constituent fragments. Is there a tool available to do that? Thanks much in advance!
-Sagar
Apologies for very slow response to your query. I am not aware of a tool that will do this. There are a couple of ways to approach this problem. If you fragment the ligands you'll need to maintain the substructual context of the atoms in contact with the protein (i.e. don't break the C-N bond of an amide). You may also be able solve the problem by atom-typing without having to fragment the molecule. Software that allows SMARTS-parsing and molecule editing will do what you want. The OEChem toolkit provides this capability but there may be other software out there that I'm not aware of.
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