-
2
-
-
0031055306
-
Geometric versus topological clustering: An insight into conformation mapping
-
DOI 10.1002/(SICI)1097-0134(199702)27:2<213::AID-PROT8>3.0.CO;2-G
-
O. M. Becker, Proteins 18PLAF 0887-3585 27, 213 (1997). 10.1002/(SICI)1097-0134(199702)27:2<213::AID-PROT8>3.0.CO;2-G (Pubitemid 27113717)
-
(1997)
Proteins: Structure, Function and Genetics
, vol.27
, Issue.2
, pp. 213-226
-
-
Becker, O.M.1
-
4
-
-
0033557181
-
Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations
-
DOI 10.1002/(SICI)1097-0134(19990215)34:3<269::AID-PROT1>3.0.CO;2-3
-
X. Daura, W. F. van Gunsteren, and A. E. Mark, Proteins 18PLAF 0887-3585 34, 269 (1999). 10.1002/(SICI)1097-0134(19990215)34:3<269::AID-PROT1>3.0. CO;2-3 (Pubitemid 29071670)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.34
, Issue.3
, pp. 269-280
-
-
Daura, X.1
Van Gunsteren, W.F.2
Mark, A.E.3
-
5
-
-
8644241573
-
Do valine side chains have an influence on the folding behavior of β-substituted β-peptides?
-
DOI 10.1002/hlca.200490223
-
A. Glättli, D. Seebach, and W. F. van Gunsteren, Helv. Chim. Acta HCACAV 0018-019X 87, 2487 (2004). 10.1002/hlca.200490223 (Pubitemid 39506764)
-
(2004)
Helvetica Chimica Acta
, vol.87
, Issue.10
, pp. 2487-2506
-
-
Glattli, A.1
Seebach, D.2
Van Gunsteren, W.F.3
-
6
-
-
0032584783
-
Reversible peptide folding in solution by molecular dynamics simulation
-
DOI 10.1006/jmbi.1998.1885
-
X. Daura, B. Jaun, D. Seebach, W. F. van Gunsteren, and A. E. Mark, J. Mol. Biol. JMOBAK 0022-2836 280, 925 (1998). 10.1006/jmbi.1998.1885 (Pubitemid 28345025)
-
(1998)
Journal of Molecular Biology
, vol.280
, Issue.5
, pp. 925-932
-
-
Daura, X.1
Jaun, B.2
Seebach, D.3
Van Gunsteren, W.F.4
Mark, A.E.5
-
7
-
-
33748267512
-
Protein under pressure: Molecular dynamics simulation of the Arc Repressor
-
DOI 10.1002/prot.21034
-
D. Trzesniak, R. D. Lins, and W. F. van Gunsteren, Proteins: Struct., Funct., Bioinf. ZZZZZZ 1097-0134 65, 136 (2006). 10.1002/prot.21034 (Pubitemid 44320623)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.1
, pp. 136-144
-
-
Trzesniak, D.1
Lins, R.D.2
Van Gunsteren, W.F.3
-
8
-
-
34247338100
-
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
-
DOI 10.1063/1.2714538
-
J. D. Chodera, N. Singhal, V. S. Pande, K. A. Dill, and W. C. Swope, J. Chem. Phys. JCPSA6 0021-9606 126, 155101 (2007). 10.1063/1.2714538 (Pubitemid 46644960)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.15
, pp. 155101
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
9
-
-
34247339716
-
Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
-
DOI 10.1063/1.2714539
-
F. Nó, I. Horenko, C. Schütte, and J. C. Smith, J. Chem. Phys. JCPSA6 0021-9606 126, 155102 (2007). 10.1063/1.2714539 (Pubitemid 46644961)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.15
, pp. 155102
-
-
Noe, F.1
Horenko, I.2
Schutte, C.3
Smith, J.C.4
-
10
-
-
39749156392
-
Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a β-sheet miniprotein
-
DOI 10.1002/prot.21565
-
S. Muff and A. Caflisch, Proteins: Struct., Funct., Bioinf. ZZZZZZ 1097-0134 70, 1185 (2008). 10.1002/prot.21565 (Pubitemid 351304079)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.4
, pp. 1185-1195
-
-
Muff, S.1
Caflisch, A.2
-
11
-
-
0009259190
-
-
JCCHDD 0192-8651,. 10.1002/(SICI)1096-987X(199912)20:16<1760::AID- JCC8>3.0.CO;2-2
-
W. Huisinga, C. Best, R. Roitzsch, C. Schütte, and F. Cordes, J. Comput. Chem. JCCHDD 0192-8651 20, 1760 (1999). 10.1002/(SICI)1096-987X(199912) 20:16<1760::AID-JCC8>3.0.CO;2-2
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1760
-
-
Huisinga, W.1
Best, C.2
Roitzsch, R.3
Schütte, C.4
Cordes, F.5
-
12
-
-
0034370539
-
-
LAAPAW 0024-3795,. 10.1016/S0024-3795(00)00095-1
-
P. Deuflhard, W. Huisinga, A. Fischer, and C. Schütte, Linear Algebr. Appl. LAAPAW 0024-3795 315, 39 (2000). 10.1016/S0024-3795(00)00095-1
-
(2000)
Linear Algebr. Appl.
, vol.315
, pp. 39
-
-
Deuflhard, P.1
Huisinga, W.2
Fischer, A.3
Schütte, C.4
-
13
-
-
84986532529
-
-
JCCHDD 0192-8651,. 10.1002/jcc.540150811
-
P. S. Shenkin and D. Q. McDonald, J. Comput. Chem. JCCHDD 0192-8651 15, 899 (1994). 10.1002/jcc.540150811
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 899
-
-
Shenkin, P.S.1
McDonald, D.Q.2
-
14
-
-
33645265985
-
-
(Wiley, New York), Vol.
-
G. M. Downs and J. M. Barnard, Reviews in Computational Chemistry (Wiley, New York, 2002), Vol. 18, pp. 1-40.
-
(2002)
Reviews in Computational Chemistry
, vol.18
, pp. 1-40
-
-
Downs, G.M.1
Barnard, J.M.2
-
15
-
-
36649006642
-
-
JCTCCE 1549-9618,. 10.1021/ct700119m
-
J. Y. Shao, S. W. Tanner, N. Thompson, and T. E. Cheatham, J. Chem. Theory Comput. JCTCCE 1549-9618 3, 2312 (2007). 10.1021/ct700119m
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2312
-
-
Shao, J.Y.1
Tanner, S.W.2
Thompson, N.3
Cheatham, T.E.4
-
16
-
-
0015680655
-
-
ITCOB4 0018-9340,. 10.1109/T-C.1973.223640
-
R. A. Jarvis and E. A. Patrick, IEEE Trans. Comput. ITCOB4 0018-9340 C-22, 1025 (1973). 10.1109/T-C.1973.223640
-
(1973)
IEEE Trans. Comput.
, vol.C-22
, pp. 1025
-
-
Jarvis, R.A.1
Patrick, E.A.2
-
17
-
-
77149177093
-
-
See supplementary material at E-JCPSA6-132-061005 for an illustration of the transformation of a sample transition matrix T to the corresponding coarse-grained transition matrix Tcg.
-
See supplementary material at 10.1063/1.3301140 E-JCPSA6-132-061005 for an illustration of the transformation of a sample transition matrix T to the corresponding coarse-grained transition matrix Tcg.
-
-
-
-
18
-
-
2942560604
-
-
JPCBFK 1089-5647,. 10.1021/jp037422q
-
W. C. Swope, J. W. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. G. Fitch, R. S. Germain, A. Rayshubski, T. J. C. Ward, Y. Zhestkov, and R. Zhou, J. Phys. Chem. B JPCBFK 1089-5647 108, 6582 (2004). 10.1021/jp037422q
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6582
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
Pitman, M.4
Eleftheriou, M.5
Fitch, B.G.6
Germain, R.S.7
Rayshubski, A.8
Ward, T.J.C.9
Zhestkov, Y.10
Zhou, R.11
-
19
-
-
34247382025
-
Long-time protein folding dynamics from short-time molecular dynamics simulations
-
DOI 10.1137/06065146X
-
J. D. Chodera, W. C. Swope, J. W. Pitera, and K. A. Dill, Multiscale Model. Simul. MMSUBT 1540-3459 5, 1214 (2006). 10.1137/06065146X (Pubitemid 350285620)
-
(2006)
Multiscale Modeling and Simulation
, vol.5
, Issue.4
, pp. 1214-1226
-
-
Chodera, J.D.1
Swope, W.C.2
Pitera, J.W.3
Dill, K.A.4
-
20
-
-
41049089101
-
-
JCPSA6 0021-9606,. 10.1063/1.2838980
-
C. H. Jensen, D. Nerukh, and R. C. Glen, J. Chem. Phys. JCPSA6 0021-9606 128, 115107 (2008). 10.1063/1.2838980
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 115107
-
-
Jensen, C.H.1
Nerukh, D.2
Glen, R.C.3
-
21
-
-
25444450005
-
Foldamer dynamics expressed via Markov state models. II. State space decomposition
-
DOI 10.1063/1.2008230, 114903
-
S. P. Elmer, S. Park, and V. S. Pande, J. Chem. Phys. JCPSA6 0021-9606 123, 114903 (2005). 10.1063/1.2008230 (Pubitemid 41377094)
-
(2005)
Journal of Chemical Physics
, vol.123
, Issue.11
, pp. 1-7
-
-
Elmer, S.P.1
Park, S.2
Pande, V.S.3
-
23
-
-
44949178407
-
-
JPCBFK 1089-5647,. 10.1021/jp0761665
-
N. -V. Buchete and G. Hummer, J. Phys. Chem. B JPCBFK 1089-5647 112, 6057 (2008). 10.1021/jp0761665
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6057
-
-
Buchete, N.-V.1
Hummer, G.2
-
24
-
-
2942567954
-
-
JPCBFK 1089-5647,. 10.1021/jp037421y
-
W. C. Swope, J. W. Pitera, and F. Suits, J. Phys. Chem. B JPCBFK 1089-5647 108, 6571 (2004). 10.1021/jp037421y
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6571
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
-
25
-
-
53849083470
-
-
CEUJED 0947-6539,. 10.1002/chem.200701380
-
R. Boned, W. F. van Gunsteren, and X. Daura, Chem.-Eur. J. CEUJED 0947-6539 14, 5039 (2008). 10.1002/chem.200701380
-
(2008)
Chem.-Eur. J.
, vol.14
, pp. 5039
-
-
Boned, R.1
Van Gunsteren, W.F.2
Daura, X.3
-
26
-
-
0003544049
-
-
(vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v., Zürich, Groningen).
-
W. F. van Gunsteren, S. R. Billeter, A. A. Eising, Biomolecular Simulation: The GROMOS96 Manual and User Guide (vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v., Zürich, Groningen, 1996).
-
(1996)
Biomolecular Simulation: The GROMOS96 Manual and User Guide
-
-
Van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
-
27
-
-
33646940952
-
-
JCTPAH 0021-9991,. 10.1016/0021-9991(77)90098-5
-
J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. JCTPAH 0021-9991 23, 327 (1977). 10.1016/0021-9991(77)90098-5
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
28
-
-
33750587438
-
-
JCPSA6 0021-9606,. 10.1063/1.448118
-
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Di Nola, and J. R. Haak, J. Chem. Phys. JCPSA6 0021-9606 81, 3684 (1984). 10.1063/1.448118
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Di Nola, A.4
Haak, J.R.5
-
29
-
-
33746878817
-
Bayesian model based clustering analysis: Application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core
-
DOI 10.1021/ci050463u
-
Y. Li, J. Chem. Inf. Model. ZZZZZZ 1549-9596 46, 1742 (2006). 10.1021/ci050463u (Pubitemid 44185699)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.4
, pp. 1742-1750
-
-
Li, Y.1
|