-
1
-
-
34249807361
-
Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation
-
Lei, H., and Y. Duan. 2007. Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. J. Phys. Chem. B. 111:5458-5463.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 5458-5463
-
-
Lei, H.1
Duan, Y.2
-
2
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution
-
Duan, Y., and P. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution. Science. 282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.2
-
3
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow, C. D., H. Nguyen, V. S. Pande, and M. Gruebele. 2002. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 420:102-106.
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
4
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling, C., B. Strockbine, and A. E. Roitberg. 2002. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124:11258-11259.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
5
-
-
0037470691
-
Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution
-
Chowdhury, S., M. C. Lee, G. Xiong, and Y. Duan. 2003. Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution. J. Mol. Biol. 327:711-717.
-
(2003)
J. Mol. Biol
, vol.327
, pp. 711-717
-
-
Chowdhury, S.1
Lee, M.C.2
Xiong, G.3
Duan, Y.4
-
6
-
-
34249298006
-
Two-stage folding of HP-35 from ab initio simulations
-
Lei, H., and Y. Duan. 2007. Two-stage folding of HP-35 from ab initio simulations. J. Mol. Biol. 370:196-206.
-
(2007)
J. Mol. Biol
, vol.370
, pp. 196-206
-
-
Lei, H.1
Duan, Y.2
-
7
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis, T., and M. Karplus. 1999. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288:477-487.
-
(1999)
J. Mol. Biol
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
8
-
-
34547298869
-
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale amber benchmarking
-
Wroblewska, L., and J. Skolnick. 2007. Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale amber benchmarking. J. Comput. Chem. 28:2059-2066.
-
(2007)
J. Comput. Chem
, vol.28
, pp. 2059-2066
-
-
Wroblewska, L.1
Skolnick, J.2
-
9
-
-
0036789950
-
Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?
-
Zhou, R., and B. J. Berne. 2002. Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? Proc. Natl. Acad. Sci. USA. 99:12777-12782.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12777-12782
-
-
Zhou, R.1
Berne, B.J.2
-
10
-
-
0141704162
-
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
-
Zhou, R. 2003. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins. 53:148-161.
-
(2003)
Proteins
, vol.53
, pp. 148-161
-
-
Zhou, R.1
-
11
-
-
33746042979
-
Structure-function-folding relationship in a WW domain
-
Jager, M., Y. Zhang, J. Bieschke, H. Nguyen, M. Dendle, M. E. Bowman, J. P. Noel, M. Gruebele, and J. W. Kelly. 2006. Structure-function-folding relationship in a WW domain. Proc. Natl. Acad. Sci. USA. 103:10648-10653.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 10648-10653
-
-
Jager, M.1
Zhang, Y.2
Bieschke, J.3
Nguyen, H.4
Dendle, M.5
Bowman, M.E.6
Noel, J.P.7
Gruebele, M.8
Kelly, J.W.9
-
12
-
-
24344464777
-
Engineering a β-sheet protein toward the folding speed limit
-
Nguyen, H., M. Jäger, J. W. Kelly, and M. Gruebele. 2005. Engineering a β-sheet protein toward the folding speed limit. J. Phys. Chem. B. 109:15182-15186.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 15182-15186
-
-
Nguyen, H.1
Jäger, M.2
Kelly, J.W.3
Gruebele, M.4
-
13
-
-
40649128566
-
An experimental survey of the transition between two-state and downhill protein folding scenarios
-
Liu, F., D. G. Du, A. A. Fuller, J. E. Davoren, P. Wipf, J. W. Kelly, and M. Gruebele. 2008. An experimental survey of the transition between two-state and downhill protein folding scenarios. Proc. Natl. Acad. Sci. USA. 105:2369-2374.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 2369-2374
-
-
Liu, F.1
Du, D.G.2
Fuller, A.A.3
Davoren, J.E.4
Wipf, P.5
Kelly, J.W.6
Gruebele, M.7
-
15
-
-
3142714765
-
-
MacKerell, A. D., Jr., M. Feig, and C. L. Brooks III. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25:1400-1415.
-
MacKerell, A. D., Jr., M. Feig, and C. L. Brooks III. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25:1400-1415.
-
-
-
-
16
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C., R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781-1802.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
17
-
-
0037137630
-
Formation of a compact structured ensemble without fluorescence signature early during ubiquitin folding
-
Qin, Z., J. Ervin, E. Larios, M. Gruebele, and H. Khara. 2002. Formation of a compact structured ensemble without fluorescence signature early during ubiquitin folding. J. Phys. Chem. B. 106:13040-13046.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 13040-13046
-
-
Qin, Z.1
Ervin, J.2
Larios, E.3
Gruebele, M.4
Khara, H.5
-
18
-
-
8644224198
-
Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations
-
Yoda, T., Y. Sugita, and Y. Okamoto. 2004. Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations. Chem. Phys. 307:269-283.
-
(2004)
Chem. Phys
, vol.307
, pp. 269-283
-
-
Yoda, T.1
Sugita, Y.2
Okamoto, Y.3
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