Series 4: Basic Search Needed on Active Compounds #87

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mattodd opened this Issue Sep 10, 2013 · 10 comments

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mattodd commented Sep 10, 2013

Taking some of the known actives in the briefing document, searches need to be done for known analogs that are either commercially available or reported in the literature.

Those sources need to then be inserted in the Wiki here:
http://openwetware.org/wiki/OpenSourceMalaria:Triazolopyrazine_%28TP%29_Series#Other_Sources_of_Compounds_in_this_Series

Chris, you interested?

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cdsouthan Sep 15, 2013

Of course, but please ask the scribes of the otherwise excellent briefing document to add the full set of molecular specifications (IUPAC,SMILES, InChI) and deposit SD files into GitHub. I have found the structures you have on the Wilki but my preliminary searches indicate they are PubChem negative. In this case, arranging a direct submission to ChEMBL Malaria, with the activity data, would obviusly be exellent for global surfacing and connectivity.

Of course, but please ask the scribes of the otherwise excellent briefing document to add the full set of molecular specifications (IUPAC,SMILES, InChI) and deposit SD files into GitHub. I have found the structures you have on the Wilki but my preliminary searches indicate they are PubChem negative. In this case, arranging a direct submission to ChEMBL Malaria, with the activity data, would obviusly be exellent for global surfacing and connectivity.

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cdsouthan Sep 28, 2013

Couldnt immediately see how to asssign the "issue" to me. Can you do that ?

Couldnt immediately see how to asssign the "issue" to me. Can you do that ?

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mattodd Sep 29, 2013

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Just tried to add you by making a team that included this repo. Didn't work. Pinging expertise of @miike

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mattodd commented Sep 29, 2013

Just tried to add you by making a team that included this repo. Didn't work. Pinging expertise of @miike

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mattodd Sep 29, 2013

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Never mind - got it.

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mattodd commented Sep 29, 2013

Never mind - got it.

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mattodd Nov 20, 2013

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We've not yet done this search, right, @cdsouthan . I'm not hassling, just making sure that you've not searched and just not uploaded. I am gradually adding info from briefing doc to Series 4 wiki, but I think we need a search on a simple compound with 1) an ether and ii) an amide in the north position. Know what I mean?

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mattodd commented Nov 20, 2013

We've not yet done this search, right, @cdsouthan . I'm not hassling, just making sure that you've not searched and just not uploaded. I am gradually adding info from briefing doc to Series 4 wiki, but I think we need a search on a simple compound with 1) an ether and ii) an amide in the north position. Know what I mean?

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sabinllm May 18, 2014

Has anyone done thorough searches in commercial databases such as Cortellis and Integrity? @PaulWillisMMV ?

Has anyone done thorough searches in commercial databases such as Cortellis and Integrity? @PaulWillisMMV ?

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cdsouthan May 18, 2014

Interesting question that I could comment on but a) could you please provenance yourself sabinllm ? (strange google hits) and b) possibly move this over to a more recent thread (since I did some PubChem searches already). As a general point @mattodd I suggest that everyone engaging here needs to be uneqivocally identifiable.

Interesting question that I could comment on but a) could you please provenance yourself sabinllm ? (strange google hits) and b) possibly move this over to a more recent thread (since I did some PubChem searches already). As a general point @mattodd I suggest that everyone engaging here needs to be uneqivocally identifiable.

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sabinllm May 18, 2014

Hi Chris! My name is Sabin Llona-Minguez. I work at the Karolinska Institute (Stockholm), I have been collaborating with OSM for a few months and I have posted here before regarding other project issues. Sorry if this is not the right thread, I have been "off the grid" lately. Could you please point me in the right direction? Cheers

Hi Chris! My name is Sabin Llona-Minguez. I work at the Karolinska Institute (Stockholm), I have been collaborating with OSM for a few months and I have posted here before regarding other project issues. Sorry if this is not the right thread, I have been "off the grid" lately. Could you please point me in the right direction? Cheers

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cdsouthan May 18, 2014

No problem Sabin. Apolgies I found u eventually on Github but oddly not directly via the glyph link. I shall try to answer the question and @mattodd could move this thread if necessary. Yes, it would certainly be interesting to mine the Thomson Reuters databases (including Integrity) under the Cortellis front-end but I'm not sure how much exclusive content it would have, they only pick up whats public after all. JFTR the Sydney team have SciFinder and I keep an eye on PubChem as well as SureChEMBL so collectively we are well covered. However,I would like to be able to search GOSTAR from GVKBIO since it is more SAR-centric than Thomson or SciFinder.

No problem Sabin. Apolgies I found u eventually on Github but oddly not directly via the glyph link. I shall try to answer the question and @mattodd could move this thread if necessary. Yes, it would certainly be interesting to mine the Thomson Reuters databases (including Integrity) under the Cortellis front-end but I'm not sure how much exclusive content it would have, they only pick up whats public after all. JFTR the Sydney team have SciFinder and I keep an eye on PubChem as well as SureChEMBL so collectively we are well covered. However,I would like to be able to search GOSTAR from GVKBIO since it is more SAR-centric than Thomson or SciFinder.

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sabinllm May 18, 2014

No worries Chris. You are right, SciFinder+PubChem+SureChEMBL is a great combo. But if you still have concerns regarding novelty/IP, I can run some searches on the Thomson Reuters databases, just to be sure.

No worries Chris. You are right, SciFinder+PubChem+SureChEMBL is a great combo. But if you still have concerns regarding novelty/IP, I can run some searches on the Thomson Reuters databases, just to be sure.

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