-
Notifications
You must be signed in to change notification settings - Fork 3
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Compounds sent for biological testing Nov 2018 #62
Comments
Great work from everyone @mbhebhe @maratsydney @david1597 @mbhebhe , it looks like there's an issue with a few of those SMILES above. Any obvious reason? Can you please correct? Great to see that these compounds are already in the Master List, including the UNC donated ones. Let's keep this issue open until we obtain the data. When that happens, post the data to ELN and link to it from here, post a graphical summary on this page below, and then link from here to the wiki, to the page "data not yet included in the wiki" so that we know the data need to be folded in. Super exciting to have all these compounds sent in. Amongst many other things, it's essential we see how the OHOH compounds do. If potent, they have the potential to become series frontrunners and we'd need to have them examined for solubility and clearance. |
@mattodd with those few SMILES, they have these symbols next to each other "[] ()". These symbols are for hyperlinking. So GH read it as a hyperlink. If there is an easier way around this please, someone let me know |
OK, nice one @mbhebhe. I wonder if quoting text works better, so that the blue hyperlink doesn't appear? @cdsouthan is there a way of testing whether these SMILES are being picked up correctly despite the inclusion of that hyperlink? Either way, the solution to this little nugget needs to be installed on the TechOps wiki before we close this issue. @mbhebhe can you please be sure to take care of that? |
I've found a fix. You need to add a backslash between [] and (). This removes the hyperlink and gives the correct smiles. For example, [C@H] (O) (space added between) will be converted to this This should make the correct SMILES searchable but can someone confirm? @mattodd I can add it to the TechOps wiki but I'll need edit access to it. |
For searching, you can check that SMILES string renders correctly in the PubChem structure search box https://pubchem.ncbi.nlm.nih.gov/search/search.cgi# . You will find the SMILES option under the "Identity/Similarity" box. Click on "Preview" and you see the image. For newer structures, you may as well do the "Search" at the same time. My guess is you can do the same in OpenBable, Chemicalize.org, Marvin, ChemDraw, and even good ole' SciFinder You should be able to do a bulk check via OpenBable or https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi but need to watch out you could still get the "wrong" rendering without an error flag |
But that doesn't work with a string that contains [] followed by () |
@edwintse the symbol used is the grave not an apostrophe |
Ah, right you are. Either way both work. |
@cdsouthan my concern was with what a search engine actually sees. If it sees the text that we see on the page, then the rendering tricks above will work. If it actually sees the underlying structure of the web page (think the binary representation of the Matrix, vs. the Woman in the Red Dress, if you will) then is there a danger that the string will be perceived with hyperlinks, graves, double brackets? And therefore be perceived wrongly? The answer to this question may be simplest to derive through experimental test. Unless the answer is obvious. |
Why not just enclose the SMILES in a <pre> tag as shown below? https://www.w3schools.com/tags/tag_pre.asp FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(NC[C@H](O)C4=CC=CC=C4)N32 |
@MFernflower we have the potency results for SGS compounds. I created a new issue for the results #65. I will close this one once we have the potency results for the USyd compounds |
#65 results are in!! |
Here is list of compounds that we have sent to Dundee.
Series 3:
OSM-S-606 is a product of the bromination of pyrrole occurring at the 7th position.
OSM-S-137 (slightly active at 1.7 uM) was re-synthesized for sending to Kansas State Uni and UNC for kinome testing.
OSM-S-145 was synthesised but not tested and came across it in the fridge.
OSM-S-649 (carboxylic analogue of OSM-S-106) that was suggested by @drc007
These molecules were made by Alfredo Picado from SGS-University of North Carolina. They are similar to our Series 3 compounds. We will see if they have any activity.
Series 4:
2018 November Dundee Compounds list.zip
The text was updated successfully, but these errors were encountered: