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From: Alessandro Contini <alessandro.contini #at# unimi.it>
Organization: Istituto di Chimica Organica
To: chemistry%!at!%ccl.net
Subject: summary of Water in Autodock 
Date: Fri, 6 Sep 2002 22:06:11 +0200
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Hi CCLers,
I summarize tips given for considering water in docking:
1. Yes it's possible. Sometimes it makes the difference between success and
    no success:
 from Dr. David van der Spoel who suggest the reading of the very exhaustive 
paper reported below

2.It is very simple: just give hydrogens (e.g. with GROMACS or REDUCE) and
  partial charges (q.kollua scriptof AD) and you can make the grid, as if
  waters were part of the protein; 
 from Csaba that suggest the same paper:

Efficient docking of peptides to proteins without prior knowledge of 
the binding site
Protein Sci 2002 11: 1729-1737


3. Try to read 
The Role of Water in Drug Design: Thymidine Kinase as Case Study
 Pavel Pospisil, Leonardo Scapozza and Gerd Folkers
 Rational Approaches to Drug Design - book of 13th European Symposium on 
Quantitative Structure-Activity Relationship, 08/2000, printed 3/2001

Alessandro
--
Dott. Alessandro Contini
Istituto di Chimica Organica, Facoltà di Farmacia
Università degli Studi di Milano
Via Venezian, 21 20133 Milano
Tel. +390250314480  Fax +390250314476
http://users.unimi.it/istchimorg/pagconthtm.htm