Dear All,
At the UGM I promised to send a reminder (mainly for Greg, but possibly
also Nik?) about the potential use of two fdef files - one with and one
without explicit hydrogens. During the demo of the PyMOL interactivity
with 3D ligand + pharmacophoric features (showfeats.py script), it was
clear that explicitly 'protonated' nitrogens (eg in a specific tautomer
of pyrrazole) were being flagged as possible hydrogen-bond acceptors, as
well as donors, due to the fdef being used recognising the potential for
a 1,2-H shift. I made the comment at the time that in cases where the
molecule had hydrogens specifically added (perhaps a docking result),
then it would probably be best to flag 'specific' rather than
'potential' Ph4 features - hence the use of separate fdef files.
My recollection (from Nik?) was that this was perhaps already the case
in NIBR user of RDKit(?)
Kind regards
James
_________________________________
Dr James Davidson
Senior Team Leader,
Medicinal & Computational Chemistry
Vernalis (R&D) Ltd
Granta Park
Great Abington
Cambridgeshire
CB21 6GB
t: +441223 895555
f: +441223 895556
d: +441223 895428
m: +447595 258005
______________________________________________________________________
PLEASE READ: This email is confidential and may be privileged. It is intended
for the named addressee(s) only and access to it by anyone else is
unauthorised. If you are not an addressee, any disclosure or copying of the
contents of this email or any action taken (or not taken) in reliance on it is
unauthorised and may be unlawful. If you have received this email in error,
please notify the sender or postmas...@vernalis.com. Email is not a secure
method of communication and the Company cannot accept responsibility for the
accuracy or completeness of this message or any attachment(s). Please check
this email for virus infection for which the Company accepts no responsibility.
If verification of this email is sought then please request a hard copy. Unless
otherwise stated, any views or opinions presented are solely those of the
author and do not represent those of the Company.
The Vernalis Group of Companies
100 Berkshire Place
Wharfedale Road
Winnersh, Berkshire
RG41 5RD, England
Tel: +44 (0)118 938 0000
To access trading company registration and address details, please go to the
Vernalis website at www.vernalis.com and click on the "Company address and
registration details" link at the bottom of the page..
______________________________________________________________________
------------------------------------------------------------------------------
Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
