summary of Water in Autodock

From: Alessandro Contini <alessandro.contini "at@at" unimi.it>
Organization: Istituto di Chimica Organica
Subject: summary of Water in Autodock
Date: Fri, 6 Sep 2002 22:06:11 +0200

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