Subject: Re: Binding energy by MM

From: John Marelius <[email-masked]>
Date: Tue, 14 Oct 1997 17:01:32 +0200 (W. Europe Daylight Time)

Hi Ramon,

you may want to take a look at the linear interaction energy (LIE) method
introduced by Åqvist et al., 1994 for calculating absolute free
energies of binding. It is a semi-empirical method which is
computationally less expensive than FEP. It is still similar to FEP in
that it is based on thermodynamic cycles and includes thermal
conformational sampling.
However, the method involves only simulations of the two physical states
(bound and free ligand) and requires no transformation processes.

The method and some applications are described in:
  Åqvist, J., Medina, C. and Samuelsson, J.E., Protein Eng., 7 (1994) 385.
  Åqvist, J. and Mowbray, S.L., J. Biol. Chem., 270 (1995) 9978.
  Åqvist, J., J. Comp. Chem., 17 (1996) 1587.
  Hultén, J., Bonham, N.M., Nillroth, U., Hansson, T., Zuccarello, G.,
Bouzide, A., Åqvist, J., Classon, B., Danielsson, H., Karlén, A.,
Kvarnström, I., Samuelsson, B. and Hallberg, A., J. Med. Chem., 40 (1997)
885.
  Hansson, T. and Åqvist, J., Protein Eng., 8 (1995) 1137.
  Hansson, T., Marelius, J. and Åqvist, J., J. Comput.-Aided Mol. Design,
1998, in press.

regards,

John Marelius

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|          John Marelius                                          |
|          Dept. of Molecular Biology, Uppsala University         |
| E-mail:  [email-masked]                                    |
| www:     http://www.ibg.uu.se/~john                             |
| address: Box 590, S-751 24 Uppsala, Sweden                      |
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