-
1
-
-
0038502170
-
Folding dynamics and mechanism of hairpin formation
-
DOI 10.1038/36626
-
V. Muoz, P. A. Thompson, J. Hofrichter, and W. A. Eaton, Nature (London) 390, 196 (1997). 10.1038/36626 (Pubitemid 27507992)
-
(1997)
Nature
, vol.390
, Issue.6656
, pp. 196-199
-
-
Munoz, V.1
Thompson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
2
-
-
0032568537
-
A statistical mechanical model for hairpin kinetics
-
DOI 10.1073/pnas.95.11.5872
-
V. Muoz, E. R. Henry, J. Hofrichter, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 95, 5872 (1998). 10.1073/pnas.95.11.5872 (Pubitemid 28248933)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.11
, pp. 5872-5879
-
-
Munoz, V.1
Henry, E.R.2
Hofrichter, J.3
Eaton, W.A.4
-
3
-
-
8644237364
-
Understanding the key factors that control the rate of hairpin folding
-
DOI 10.1073/pnas.0405904101
-
D. Du, Y. Zhu, C. Huang, and F. Gai, Proc. Natl. Acad. Sci. U.S.A. 101, 15915 (2004). 10.1073/pnas.0405904101 (Pubitemid 39507902)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.45
, pp. 15915-15920
-
-
Du, D.1
Zhu, Y.2
Huang, C.-Y.3
Gai, F.4
-
4
-
-
1642570290
-
Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy
-
DOI 10.1073/pnas.0305260101
-
C. Snow, L. Qiu, D. Du, F. Gai, S. Hagen, and V. Pande, Proc. Natl. Acad. Sci. U.S.A. 101, 4077 (2004). 10.1073/pnas.0305260101 (Pubitemid 38405886)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.12
, pp. 4077-4082
-
-
Snow, C.D.1
Qiu, L.2
Du, D.3
Gai, F.4
Hagen, S.J.5
Pande, V.S.6
-
5
-
-
18844361915
-
Helix-coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures
-
DOI 10.1002/prot.20439
-
S. Gnanakaran and A. Garcia, Proteins: Struct., Funct., Bioinf. 59, 773 (2005). 10.1002/prot.20439 (Pubitemid 40695852)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 773-782
-
-
Gnanakaran, S.1
Garcia, A.E.2
-
6
-
-
20544435097
-
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
-
DOI 10.1529/biophysj.104.051938
-
E. Sorin and V. Pande, Biophys. J. 88, 2472 (2005). 10.1529/biophysj.104. 051938 (Pubitemid 40976118)
-
(2005)
Biophysical Journal
, vol.88
, Issue.4
, pp. 2472-2493
-
-
Sorin, E.J.1
Pande, V.S.2
-
7
-
-
77956302920
-
-
10.1371/journal.pone.0010056
-
E. Thompson, A. DePaul, S. Patel, and E. Sorin, PloS ONE 5, e10056 (2010). 10.1371/journal.pone.0010056
-
(2010)
PloS ONE
, vol.5
, pp. 10056
-
-
Thompson, E.1
Depaul, A.2
Patel, S.3
Sorin, E.4
-
8
-
-
0035826776
-
Tryptophan zippers: Stable, monomeric hairpins
-
DOI 10.1073/pnas.091100898
-
A. Cochran, N. Skelton, and M. Starovasnik, Proc. Natl. Acad. Sci. U.S.A. 98, 5578 (2001). 10.1073/pnas.091100898 (Pubitemid 32435684)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.10
, pp. 5578-5583
-
-
Cochran, A.G.1
Skelton, N.J.2
Starovasnik, M.A.3
-
9
-
-
70350495817
-
-
10.1021/bi901249d
-
L. Wu, D. McElheny, R. Huang, and T. A. Keiderling, Biochemistry 48, 10362 (2009). 10.1021/bi901249d
-
(2009)
Biochemistry
, vol.48
, pp. 10362
-
-
Wu, L.1
McElheny, D.2
Huang, R.3
Keiderling, T.A.4
-
10
-
-
49549116236
-
-
10.1080/08927020801947020
-
W. Xu, Y. Yang, Y. Mu, and L. Nordenskiold, Mol. Simul. 34, 575 (2008). 10.1080/08927020801947020
-
(2008)
Mol. Simul.
, vol.34
, pp. 575
-
-
Xu, W.1
Yang, Y.2
Mu, Y.3
Nordenskiold, L.4
-
11
-
-
0347130904
-
Heterogeneous Folding of the trpzip Hairpin: Full Atom Simulation and Experiment
-
DOI 10.1016/j.jmb.2003.11.033
-
W. Yang, J. Pitera, W. Swope, and M. Gruebele, J. Mol. Biol. 336, 241 (2004). 10.1016/j.jmb.2003.11.033 (Pubitemid 38102345)
-
(2004)
Journal of Molecular Biology
, vol.336
, Issue.1
, pp. 241-251
-
-
Yang, W.Y.1
Pitera, J.W.2
Swope, W.C.3
Gruebele, M.4
-
12
-
-
31944442794
-
Folding mechanism of hairpins studied by replica exchange molecular simulations
-
DOI 10.1002/prot.20813
-
J. Zhang, M. Qin, and W. Wang, Proteins: Struct., Funct., Bioinf. 62, 672 (2006). 10.1002/prot.20813 (Pubitemid 43191254)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.62
, Issue.3
, pp. 672-685
-
-
Zhang, J.1
Qin, M.2
Wang, W.3
-
13
-
-
40049089464
-
Observation of multiple folding pathways of hairpin trpzip2 from independent continuous folding trajectories
-
DOI 10.1093/bioinformatics/btn029
-
C. Chen and Y. Xiao, Bioinformatics 24, 659 (2008). 10.1093/ bioinformatics/btn029 (Pubitemid 351321209)
-
(2008)
Bioinformatics
, vol.24
, Issue.5
, pp. 659-665
-
-
Chen, C.1
Xiao, Y.2
-
16
-
-
67149138047
-
-
10.1021/jp806749b
-
H. Nymeyer, J. Phys. Chem. B 113, 8288 (2009). 10.1021/jp806749b
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 8288
-
-
Nymeyer, H.1
-
17
-
-
0000626498
-
-
10.1002/(SICI)1096-987X(20000715)21:9748::AID-JCC43.0.CO;2-2
-
S. Ono, N. Nakajima, J. Higo, and H. Nakamura, J. Comput. Chem. 21, 748 (2000). 10.1002/(SICI)1096-987X(20000715)21:9748::AID-JCC43.0.CO;2-2
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 748
-
-
Ono, S.1
Nakajima, N.2
Higo, J.3
Nakamura, H.4
-
19
-
-
0037340910
-
-
10.1016/S0006-3495(03)74966-2
-
S. Gnanakaran and A. E. Garcia, Biophys. J. 84, 1548 (2003). 10.1016/S0006-3495(03)74966-2
-
(2003)
Biophys. J.
, vol.84
, pp. 1548
-
-
Gnanakaran, S.1
Garcia, A.E.2
-
21
-
-
0001398008
-
-
10.1002/1096-987X(200009)21:121049::AID-JCC33.0.CO;2-F
-
J. Wang, P. Cieplak, and P. Kollman, J. Comput. Chem. 21, 1049 (2000). 10.1002/1096-987X(200009)21:121049::AID-JCC33.0.CO;2-F
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.3
-
22
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
DOI 10.1002/prot.21123
-
V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, Proteins: Struct., Funct., Bioinf. 65, 712 (2006). 10.1002/prot.21123 (Pubitemid 44583220)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.3
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
23
-
-
0003495725
-
-
(Elsevier, New York)
-
P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot, and A. Pohorille, Computer Simulation of Biomolecular Systems (Elsevier, New York, 1997) pp. 83-96.
-
(1997)
Computer Simulation of Biomolecular Systems
, pp. 83-96
-
-
Kollman, P.1
Dixon, R.2
Cornell, W.3
Fox, T.4
Chipot, C.5
Pohorille, A.6
-
24
-
-
0029011701
-
-
10.1021/ja00124a002
-
W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995). 10.1021/ja00124a002
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
26
-
-
0034701222
-
Molecular dynamics simulations of nucleic acids with a generalized born solvation model
-
DOI 10.1021/ja9939385
-
V. Tsui and D. Case, J. Am. Chem. Soc. 122, 2489 (2000). 10.1021/ja9939385 (Pubitemid 30211961)
-
(2000)
Journal of the American Chemical Society
, vol.122
, Issue.11
, pp. 2489-2498
-
-
Tsui, V.1
Case, D.A.2
-
27
-
-
0033654297
-
-
10.1146/annurev.physchem.51.1.129
-
D. Bashford and D. Case, J. Phys. Chem. 51, 129 (2000). 10.1146/annurev.physchem.51.1.129
-
(2000)
J. Phys. Chem.
, vol.51
, pp. 129
-
-
Bashford, D.1
Case, D.2
-
28
-
-
0344778061
-
-
10.1021/ja00172a038
-
W. Still, A. Tempczyk, R. Hawley, and T. Hendrickson, J. Am. Chem. Soc. 112, 6127 (1990). 10.1021/ja00172a038
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127
-
-
Still, W.1
Tempczyk, A.2
Hawley, R.3
Hendrickson, T.4
-
29
-
-
0032484151
-
Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
-
DOI 10.1006/jmbi.1998.2172
-
M. Schaefer, C. Bartels, and M. Karplus, J. Mol. Biol. 284, 835 (1998). 10.1006/jmbi.1998.2172 (Pubitemid 28550026)
-
(1998)
Journal of Molecular Biology
, vol.284
, Issue.3
, pp. 835-848
-
-
Schaefer, M.1
Bartels, C.2
Karplus, M.3
-
30
-
-
64649105762
-
-
10.1002/jcc.21209
-
M. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. Legrand, A. Beberg, D. Ensign, C. Bruns, and V. Pande, J. Comput. Chem. 30, 864 (2009). 10.1002/jcc.21209
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 864
-
-
Friedrichs, M.1
Eastman, P.2
Vaidyanathan, V.3
Houston, M.4
Legrand, S.5
Beberg, A.6
Ensign, D.7
Bruns, C.8
Pande, V.9
-
31
-
-
79551646198
-
-
https://simtk.org/home/pyopenmm (2010).
-
(2010)
-
-
-
33
-
-
79551628370
-
-
AMBER 11, University of California, San Francisco
-
D. Case, T. Darden, I. T. E. Cheatham, C. Simmerling, J. Wang, R. Duke, R. Luo, R. Walker, W. Zhang, K. Merz, B. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvry, K. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. Roe, D. Mathews, M. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P. Kollman, AMBER 11, University of California, San Francisco, 2010.
-
(2010)
-
-
Case, D.1
Darden, T.2
Cheatham, I.T.E.3
Simmerling, C.4
Wang, J.5
Duke, R.6
Luo, R.7
Walker, R.8
Zhang, W.9
Merz, K.10
Roberts, B.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossvry, I.16
Wong, K.17
Paesani, F.18
Vanicek, J.19
Liu, J.20
Wu, X.21
Brozell, S.22
Steinbrecher, T.23
Gohlke, H.24
Cai, Q.25
Ye, X.26
Wang, J.27
Hsieh, M.-J.28
Cui, G.29
Roe, D.30
Mathews, D.31
Seetin, M.32
Sagui, C.33
Babin, V.34
Luchko, T.35
Gusarov, S.36
Kovalenko, A.37
Kollman, P.38
more..
-
34
-
-
0001616080
-
-
10.1016/S0009-2614(99)01123-9
-
Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999). 10.1016/S0009-2614(99)01123-9
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141
-
-
Sugita, Y.1
Okamoto, Y.2
-
37
-
-
0036394906
-
Native-like mean structure in the unfolded ensemble of small proteins
-
DOI 10.1016/S0022-2836(02)00888-4
-
B. Zagrovic, C. Snow, S. Khaliq, M. Shirts, and V. Pande, J. Mol. Biol. 323, 153 (2002). 10.1016/S0022-2836(02)00888-4 (Pubitemid 35168488)
-
(2002)
Journal of Molecular Biology
, vol.323
, Issue.1
, pp. 153-164
-
-
Zagrovic, B.1
Snow, C.D.2
Khaliq, S.3
Shirts, M.R.4
Pande, V.S.5
-
40
-
-
0141704162
-
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
-
DOI 10.1002/prot.10483
-
R. Zhou, Proteins: Struct., Funct., Genet. 53, 148 (2003). 10.1002/prot.10483 (Pubitemid 37193811)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.53
, Issue.2
, pp. 148-161
-
-
Zhou, R.1
-
42
-
-
33847723384
-
Secondary structure bias in generalized born solvent models: Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation
-
DOI 10.1021/jp066831u
-
D. R. Roe, A. Okur, L. Wickstrom, V. Hornak, and C. Simmerling, J. Phys. Chem. B 111, 1846 (2007). 10.1021/jp066831u (Pubitemid 46384278)
-
(2007)
Journal of Physical Chemistry B
, vol.111
, Issue.7
, pp. 1846-1857
-
-
Roe, D.R.1
Okur, A.2
Wickstrom, L.3
Hornak, V.4
Simmerling, C.5
-
43
-
-
16844371842
-
Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed hairpin "trpzip2"
-
DOI 10.1021/ja043492e
-
O. Guvench and C. Brooks, J. Am. Chem. Soc. 127, 4668 (2005). 10.1021/ja043492e (Pubitemid 40489623)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.13
, pp. 4668-4674
-
-
Guvench, O.1
Brooks III, C.L.2
|