Hi Folks, We are building a tool that generates libraries of compounds based on a list of reactants and a set of compatible reactants, and allows selection of the products. We define the process as "product-based reactant selection" from an old paper (at the end of the day we need to make these compounds!) We call the product "Library Design Tool" considering the Design composed of generation (enumeration) and selection phases. Our people got used to the term reaction-based enumeration (but I am not sure if they still distinguish from R-Group-Enumeration), virtual products and the like, but in hindsight in silico synthesis ... definitely not bad.
Cheeers, m Il giorno ven 25 set 2020 alle ore 15:26 Ivan Tubert-Brohman < ivan.tubert-broh...@schrodinger.com> ha scritto: > We use "reaction-based enumeration" to distinguish it from "R-group > enumeration". Both are types of virtual library enumeration. > > R-group enumeration allows you to attach any R-group anywhere. It is > simple and fast but you can easily create implausible (or hard to > synthesize) molecules if you are not careful. > > Reaction-based enumeration at least guarantees that you already have > reactants with the right functional groups in the right places, and if you > make your reactions sophisticated enough you can even check for other > disqualifying conditions such as interfering functional groups. > > Of course in a context where it is not immediately obvious that you are > talking about doing it on a computer, I suppose something along the lines > of "virtual reaction-based enumeration" might make sense. > > Best, > Ivan > > > On Fri, Sep 25, 2020 at 4:26 AM Thomas Strunz <beginn...@hotmail.de> > wrote: > >> Hi Brian, >> >> commercial tools usually use the term "reaction-based enumeration" or >> "reaction-based library design". >> >> Best Regards, >> >> Thomas >> >> ------------------------------ >> *Von:* Bennion, Brian via Rdkit-discuss < >> rdkit-discuss@lists.sourceforge.net> >> *Gesendet:* Freitag, 25. September 2020 07:19 >> *An:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net> >> *Betreff:* [Rdkit-discuss] proper technical term for generating virtual >> compounds with rdkit and smarts >> >> hello >> >> I have a paper in review and is intended for a large audience that has >> synthetic chemists, biologist and comp chem. >> One reviewer had issues with the term in-silico syntheses. >> I used rdkit and smarts reactions to generate large libraries of >> compounds for our research project. Is there a better term to use? I feel >> "chemical enumeration" is just as foreign. >> >> The abstract is below. >> >> The current standard treatment for organophosphate poisoning primarily >> relies on the use of small molecule-based oximes that can efficiently >> restore acetylcholinesterase (AChE) activity. Despite their efficacy in >> reactivating AChE, the action of drugs like 2-pralidoxime (2-PAM) is >> primarily limited to the peripheral nervous system (PNS) and, thus, >> provides no protection to the central nervous system (CNS). This lack >> of action in the CNS stems from the ionic nature of the drugs; they >> cannot cross the blood-brain barrier (BBB) to access to any nerve >> agent-inhibited AChE therein. In this report, we present a small >> molecule oxime, called LLNL-02, that can diffuse across the BBB for >> reactivation of nerve agent-inhibited AChE in the CNS. Our >> candidate-development >> approach utilizes a combination of parallel chemical and in - silico >> syntheses, computational modeling, and a battery of detailed in vitro >> and in vivo assessments that have identified LLNL-02 as a top CNS-active >> candidate >> against nerve agent poisoning. Additional experiments to determine acute >> and chronic toxicity as required for regulatory approval are ongoing. >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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