Although many computational methods have been proposed for predicting protein–protein complex structures, the prediction remains difficult at the atomic level. In this study, we applied a simple ensemble docking method to the complex of hen egg white lysozyme and its antibody (HyHEL-10). Although this method took into account the protein conformational ensemble, the result was not better than that of a typical rigid docking calculation. In the decomposition analysis, however, we found energetic minima near the crystal structure for a few conformation pairs. This may imply that conformational selection is essential during the early stage of binding.

1.
A.
Beck
,
T.
Wurch
,
C.
Bailly
and
N.
Corvaia
,
Nature Reviews Immunology
10
,
345
352
(
2010
).
2.
M.
Zacharias
,
Curr. Opin. Struct. Biol.
20
,
180
186
(
2010
).
3.
M.
Shiroishi
,
K.
Tsumoto
,
Y.
Tanaka
,
A.
Yokota
,
T.
Nakanishi
,
H.
Kondo
and
I.
Kumagai
,
J. Biol. Chem.
282
,
6783
6791
(
2007
).
4.
T.
Yamashita
,
Biomedical Sciences
2
,
34
47
(
2016
).
5.
T.
Yamashita
,
AIP Conf. Proc.
1790
,
020026
(
2016
).
6.
T.
Yamashita
and
H.
Fujitani
,
Chem. Phys. Lett.
609
,
50
53
(
2014
).
7.
T.
Nakayama
,
E.
Mizohata
,
T.
Yamashita
,
S.
Nagatoishi
,
M.
Nakakido
,
H.
Iwanari
,
Y.
Mochizuki
,
Y.
Kado
,
Y.
Yokota
,
R.
Satoh
,
K.
Tsumoto
,
H.
Fujitani
,
T.
Kodama
,
T.
Hamakubo
and
T.
Inoue
,
Protein Sci.
24
,
328
340
(
2015
).
8.
T.
Yamashita
and
G. A.
Voth
,
J. Phys. Chem. B
114
,
592
603
(
2010
).
9.
T.
Yamashita
and
G. A.
Voth
,
J. Am. Chem. Soc.
134
,
1147
1152
(
2012
).
10.
T.
Yamashita
,
JPS Conf. Proc.
1
,
013086
(
2014
).
11.
J.
Xu
,
T.
Yamashita
,
N.
Agmon
and
G. A.
Voth
,
J. Phys. Chem. B
117
,
15426
15435
(
2013
).
12.
T.
Sakano
,
M. I.
Mahamood
,
T.
Yamashita
and
H.
Fujitani
,
Biophys. Physicobiol.
13
,
181
194
(
2016
).
13.
T.
Yamashita
,
A.
Ueda
,
T.
Mitsui
,
A.
Tomonaga
,
S.
Matsumoto
,
T.
Kodama
and
H.
Fujitani
,
Chem. Pharm. Bull.
63
,
147
155
(
2015
).
14.
T.
Yamashita
,
A.
Ueda
,
T.
Mitsui
,
A.
Tomonaga
,
S.
Matsumoto
,
T.
Kodama
and
H.
Fujitani
,
Chem. Pharm. Bull.
62
,
661
667
(
2014
).
15.
H.
Fujitani
,
A.
Matsuura
,
S.
Sakai
,
H.
Sato
and
Y.
Tanida
,
J. Chem. Theory Comput.
5
,
1155
1165
(
2009
).
16.
T.
Yamashita
,
JPS Conf. Proc.
5
,
010003
(
2015
).
17.
S.
Pronk
,
S.
Pall
,
R.
Schulz
,
P.
Larsson
,
P.
Bjelkmar
,
R.
Apostolov
,
M. R.
Shirts
,
J. C.
Smith
,
P. M.
Kasson
,
D.
van der Spoel
,
B.
Hess
and
E.
Lindahl
,
Bioinformatics
29
,
845
854
(
2013
).
18.
R.
Chen
,
L.
Li
and
Z.
Weng
,
Proteins: Structure, Function, and Bioinformatics
52
,
80
87
(
2003
).
19.
A. G.
Schmidt
,
H.
Xu
,
A. R.
Khan
,
T.
O’Donnell
,
S.
Khurana
,
L. R.
King
,
J.
Manischewitz
,
H.
Golding
,
P.
Suphaphiphat
and
A.
Carfi
,
Proceedings of the National Academy of Sciences
110
,
264
269
(
2013
).
20.
S.
Chaudhury
and
J. J.
Gray
,
J. Mol. Biol.
381
,
1068
1087
(
2008
).
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