Subject: molecular similarity

From: Antoine Logean <[email-masked]>
Date: Mon, 05 Aug 2002 12:43:01 +0200

Dear all,

Imagine a chemist come to you ( you, the strange person who does strange 
things with computers ! - the organic chemists have really a primitive 
view of our work ! any way it is an other story ) with two molecules on 
a paper and he want to know the "similarity" between the two molecules 
(for which we have no idea of the receptor 3D structure). Imagine you do 
not want to investigate more as 10 hours (a day) to the thing. What 
would you do ?

Until know I just build the two 3D molecular models (20 minutes). So I 
have still 9 hours and 40 minutes for the thing. (minus 10 minutes for 
this mail). What can I do ? I plan to :

1) first fit the two molecules (two glycolypids). If this task until now 
was trivial (I mainly work with protein) I realize that for two organic 
compounds with not necessary the same scaffold, it is not an easy   job 
! I will use FlexS. But I would prefer to use a free program. Do you 
have any suggestions ? (most programs I know are good to handle proteins 
  but not organic compounds.)

2) after fitting I will measure : the polar and apolar surface, the 
solvation energy, the number of H donnor/acceptor and the molecular 
volume. Perhaps if I have time I will make a dynamic with Amber to have 
an idea of the "rigidity" of the two molecules.

I am sure that "old dinosaurs" in the modeling field can give me good 
hints in order to spend 10 hours and not 10 days on a project that has 1 
chance over 1000 to be realized.

Thank you

Antoine