Re: WSN: effective hydrophobic forces (fwd)

To: Water Science Network <water@gibbs.oit.unc.edu>
Subject: Re: WSN: effective hydrophobic forces (fwd)
From: Water Science Network Administrator <wsn-adm@mmlds1.pha.unc.edu>
Date: Fri, 4 Mar 1994 11:14:51 -0500 (EST)

Sender: stoutepf@chemsci1.es.dupont.com (Pieter Stouten)
Subject: Re: WSN: effective hydrophobic forces

Hi David,

>I am trying to develop a good model for the hydrophobic
>potential of mean force between apolar things in water.
>I intend to use this to approximate the effective hydrophobic
>forces between hydrophobic amino acid residues for protein
>structure prediction.
>
We have developed a solvation model based on accessible volumes
rather than surface areas which is very fast (about six times
faster than the fastest surface area approach) which as far
as I can deduce from your question does exactly what you want.

Relevant papers are:
* P.F.W. Stouten, C. Froemmel, H. Nakamura & C. Sander, "An Effective
  Solvation Term Based on Atomic Occupancies for Use in Protein
  Simulations," Mol. Simulation 10 (1993) 97-120.
* B.A. Luty, M. Zacharias, Z.R. Wasserman, P.F.W. Stouten, C.N. Hodge &
  J.A. McCammon, "Estimating Receptor-Ligand Interaction Energies Using
  a Combined Molecular Mechanics/Grid Method." Will be submitted to
  J. Comp. Chem. soon.

Just let me know if you want a reprint of the Mol. Sim. paper.
Hope this helps.


Cheers, Pieter.

 
Pieter Stouten, Senior Research Scientist    ||
Computer Aided Drug Design Group             ||
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