Mean field approximation is employed for accurate calculation of free energy differences. Significantly enhanced sampling is obtained for local changes. In an example for the mutation of a residue in a protein, the increase in the sampling yielded converged results at a significantly lower computational cost than the usual approach.

1.
The field is very active and therefore we list below only five review articles:
(a)
D. L.
Beveridge
and
F. M.
Dicapia
,
Annu. Rev. Biophys. Chem.
18
,
431
(
1989
);
(b)
W. L.
Jorgensen
,
Acc. Chem. Res.
22
,
184
(
1989
);
(c)
P. A.
Kollman
and
K. M.
Mertz
,
Acc. Chem. Res.
23
,
246
(
1990
);
(d)
W. F.
van-Gunsteren
and
H. J. C.
Berendsen
,
Angew. Chem. Int. Ed. Engl.
29
,
992
(
1990
);
(e)
T. P.
Straatsma
and
J. A.
McCammon
,
Annu. Rev. Phys. Chem.
43
,
407
(
1992
).
2.
E. G.
Arutyunyan
,
I. P.
Kuranova
,
B. K.
Vainstein
, and
W.
Steigmann
,
Sov. Phys. Crystallogr.
25
,
43
(
1980
).
3.
R.
Czerminski
and
R.
Elber
,
Proteins
10
,
70
(
1991
);
W.
Nowak
,
R.
Czerminski
, and
R.
Elber
,
J. Am. Chem. Soc.
113
,
5627
(
1991
);
G.
Verkhivker
,
R.
Elber
, and
Q. H.
Gibson
,
J. Am. Chem. Soc.
114
,
7866
(
1992
).
4.
G. Verkhivker and R. Elber (work in progress).
5.
A.
Roitberg
and
R.
Elber
,
J. Chem. Phys.
85
,
9277
(
1991
).
6.
W. F. van-Gunsteren, in Computer Simulation of Biomolecular Systems:Theoretical and Experimental Applications, edited by W. F. van-Gunsteren and P. K. Weinger (ESCOM Science, 1989), p. 27.
7.
R. Elber, A. Roitberg, G. Verkhivker, R. Goldstein, H. Li, and C. Simmerling, “MOIL: A Molecular Dynamics Program with Emphasis on Reaction Path Calculations and Conformational Searches in Proteins,” in Advances in Computational Biology, edited by H. Villar (JAI, Greenwich, 1993) (in preparation). The program is available via anonymous ftp from 128.248.186.70.
8.
S. J.
Weiner
,
P. A.
Kollman
,
D. A.
Case
,
U. C.
Singh
,
C.
Ghio
,
G.
Alagona
,
S.
Profeta
, and
P.
Weiner
,
J. Am. Chem. Soc.
106
,
765
(
1984
).
9.
W. L.
Jorgensen
and
J.
Tirado-Rives
,
J. Am. Chem. Soc.
110
,
1657
(
1988
).
10.
B. R.
Brooks
,
R. E.
Bruccoleri
,
B. D.
Olafson
,
D. J.
States
,
S.
Swaminathan
, and
M.
Karplus
,
J. Comput. Chem.
4
,
187
(
1983
).
11.
J. P.
Ryckaert
,
G.
Ciccotti
, and
H. J. C.
Berendsen
,
J. Comput. Phys.
23
,
327
(
1977
).
This content is only available via PDF.
You do not currently have access to this content.