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
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
Hello, all
I have written a script which extracts certain residues from a PDB file, and
writes them out to a new PDB-file.
The script looks like this:
from rdkit import Chem
def create_sub_mol(mol_in, mol_in_conf, bs_atom_list):
"""
Creates a mol of given atoms atoms, e.g. the atoms
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
Gesendet: Freitag, 25. September 2020 07:19
An: RDKit Discuss
Betreff: [Rdkit-discuss]
Hello Brian,
On Fri, 25 Sep 2020 05:19:14 +
"Bennion, Brian via Rdkit-discuss"
wrote:
> 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
I recall the first time I heard the term was in a project meeting in
RiboTargets back in around 1999/2000. One of our modelling group used it
after hearing discussion of results of in vitro and in vivo studies being
discussed. My recollection is that there was a certain amount of amusement
at
Without your more detailled explanation of what that term specifically
means I was wondering too at first. But then I did the most obvious
thing: search for it online and found
https://scholar.google.com/scholar?q=%22in+silico+synthesis%22=en_sdt=0_vis=1=scholart
. Looks to me other people use
I actually like *in silico* synthesis - though I don't think I've seen it
before - but I can imagine a chemist finding it objectionable.
I would probably use "virtual library enumeration"
-greg
On Fri, Sep 25, 2020 at 7:21 AM Bennion, Brian via Rdkit-discuss <
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