-
3
-
-
33748248896
-
Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece
-
Jayachandran G., Vishal V., and Pande V.S. Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J. Chem. Phys. 124 (2006) 164902
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 164902
-
-
Jayachandran, G.1
Vishal, V.2
Pande, V.S.3
-
4
-
-
1942505724
-
Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements
-
Vermeulen W., Vanhaesebrouck P., Van Troys M., Verschueren M., Fant F., Goethals M., et al. Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements. Protein Sci. 13 (2004) 1276-1287
-
(2004)
Protein Sci.
, vol.13
, pp. 1276-1287
-
-
Vermeulen, W.1
Vanhaesebrouck, P.2
Van Troys, M.3
Verschueren, M.4
Fant, F.5
Goethals, M.6
-
5
-
-
0031058410
-
NMR structure of the 35-residue villin headpiece subdomain
-
McKnight C.J., Matsudaira P.T., and Kim P.S. NMR structure of the 35-residue villin headpiece subdomain. Nat. Struct. Biol. 4 (1997) 180-184
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 180-184
-
-
McKnight, C.J.1
Matsudaira, P.T.2
Kim, P.S.3
-
6
-
-
33745228454
-
Identification of the PXW sequence as a structural gatekeeper of the headpiece C-terminal subdomain fold
-
Vermeulen W., Van Troys M., Bourry D., Dewitte D., Rossenu S., Goethals M., et al. Identification of the PXW sequence as a structural gatekeeper of the headpiece C-terminal subdomain fold. J. Mol. Biol. 359 (2006) 1277-1292
-
(2006)
J. Mol. Biol.
, vol.359
, pp. 1277-1292
-
-
Vermeulen, W.1
Van Troys, M.2
Bourry, D.3
Dewitte, D.4
Rossenu, S.5
Goethals, M.6
-
7
-
-
0036180616
-
The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain
-
Frank B.S., Vardar D., Buckley D.A., and McKnight C.J. The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain. Protein Sci. 11 (2002) 680-687
-
(2002)
Protein Sci.
, vol.11
, pp. 680-687
-
-
Frank, B.S.1
Vardar, D.2
Buckley, D.A.3
McKnight, C.J.4
-
8
-
-
0036428782
-
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
-
Zagrovic B., Snow C.D., Shirts M.R., and Pande V.S. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323 (2002) 927-937
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 927-937
-
-
Zagrovic, B.1
Snow, C.D.2
Shirts, M.R.3
Pande, V.S.4
-
9
-
-
2542462060
-
Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH
-
Ripoll D.R., Vila J.A., and Scheraga H.A. Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. J. Mol. Biol. 339 (2004) 915-925
-
(2004)
J. Mol. Biol.
, vol.339
, pp. 915-925
-
-
Ripoll, D.R.1
Vila, J.A.2
Scheraga, H.A.3
-
10
-
-
0345724787
-
Ab initio folding of helix bundle proteins using molecular dynamics simulations
-
Jang S.M., Kim E., Shin S., and Pak Y. Ab initio folding of helix bundle proteins using molecular dynamics simulations. J. Am. Chem. Soc. 125 (2003) 14841-14846
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 14841-14846
-
-
Jang, S.M.1
Kim, E.2
Shin, S.3
Pak, Y.4
-
11
-
-
27144440086
-
Efficient sampling of protein structures by model hopping
-
Kwak W., and Hansmann U.H.E. Efficient sampling of protein structures by model hopping. Phys. Rev. Lett. 95 (2005) 138102
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 138102
-
-
Kwak, W.1
Hansmann, U.H.E.2
-
12
-
-
34249298006
-
Two-stage folding of HP-35 from ab initio simulations
-
Lei H., and Duan Y. Two-stage folding of HP-35 from ab initio simulations. J. Mol. Biol. 370 (2007) 196-206
-
(2007)
J. Mol. Biol.
, vol.370
, pp. 196-206
-
-
Lei, H.1
Duan, Y.2
-
13
-
-
11344285181
-
Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics
-
DeMori G.M., Colombo G., and Micheletti C. Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins: Struct. Funct. Genet. 58 (2005) 459-471
-
(2005)
Proteins: Struct. Funct. Genet.
, vol.58
, pp. 459-471
-
-
DeMori, G.M.1
Colombo, G.2
Micheletti, C.3
-
14
-
-
1142279630
-
Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid
-
Mukherjee A., and Bagchi B. Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid. J. Chem. Phys. 120 (2004) 1602-1612
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 1602-1612
-
-
Mukherjee, A.1
Bagchi, B.2
-
16
-
-
33645683978
-
Global optimization and folding pathways of selected alpha-helical proteins
-
Carr J.M., and Wales D.J. Global optimization and folding pathways of selected alpha-helical proteins. J. Chem. Phys. 123 (2005) 234901
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 234901
-
-
Carr, J.M.1
Wales, D.J.2
-
17
-
-
0346665548
-
Large-scale context in protein folding: villin headpiece
-
Fernandez A., Shen M.Y., Colubri A., Sosnick T.R., Berry R.S., and Freed K.F. Large-scale context in protein folding: villin headpiece. Biochemistry 42 (2003) 664-671
-
(2003)
Biochemistry
, vol.42
, pp. 664-671
-
-
Fernandez, A.1
Shen, M.Y.2
Colubri, A.3
Sosnick, T.R.4
Berry, R.S.5
Freed, K.F.6
-
18
-
-
34249071886
-
A bias-exchange approach to protein folding
-
Piana S., and Laio A. A bias-exchange approach to protein folding. J. Phys. Chem. B 111 (2007) 4553-4559
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 4553-4559
-
-
Piana, S.1
Laio, A.2
-
19
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314 (1999) 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
21
-
-
34247639441
-
Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations
-
Lei H., Wu C., Liu H., and Duan Y. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proc. Natl Acad. Sci. USA 104 (2007) 4925-4930
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 4925-4930
-
-
Lei, H.1
Wu, C.2
Liu, H.3
Duan, Y.4
-
22
-
-
0027991081
-
Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation
-
Lee K.H., Xie D., Freire E., and Amzel L.M. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins: Struct. Funct. Genet. 20 (1994) 68-84
-
(1994)
Proteins: Struct. Funct. Genet.
, vol.20
, pp. 68-84
-
-
Lee, K.H.1
Xie, D.2
Freire, E.3
Amzel, L.M.4
-
23
-
-
0029900846
-
The magnitude of the backbone conformational entropy change in protein folding
-
D'Aquino J.A., Gomez J., Hilser V.J., Lee K.H., Amzel L.M., and Freire E. The magnitude of the backbone conformational entropy change in protein folding. Proteins: Struct. Funct. Genet. 25 (1996) 143-156
-
(1996)
Proteins: Struct. Funct. Genet.
, vol.25
, pp. 143-156
-
-
D'Aquino, J.A.1
Gomez, J.2
Hilser, V.J.3
Lee, K.H.4
Amzel, L.M.5
Freire, E.6
-
24
-
-
0029957505
-
The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations
-
Hilser V.J., Gomez J., and Freire E. The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations. Proteins: Struct. Funct. Genet. 26 (1996) 123-133
-
(1996)
Proteins: Struct. Funct. Genet.
, vol.26
, pp. 123-133
-
-
Hilser, V.J.1
Gomez, J.2
Freire, E.3
-
25
-
-
0029958659
-
Structure-based thermodynamic scale of alpha-helix propensities in amino acids
-
Luque I., Mayorga O.L., and Freire E. Structure-based thermodynamic scale of alpha-helix propensities in amino acids. Biochemistry 35 (1996) 13681-13688
-
(1996)
Biochemistry
, vol.35
, pp. 13681-13688
-
-
Luque, I.1
Mayorga, O.L.2
Freire, E.3
-
26
-
-
0030905238
-
Structure-based thermodynamic analysis of HIV-1 protease inhibitors
-
Bardi J.S., Luque I., and Freire E. Structure-based thermodynamic analysis of HIV-1 protease inhibitors. Biochemistry 36 (1997) 6588-6596
-
(1997)
Biochemistry
, vol.36
, pp. 6588-6596
-
-
Bardi, J.S.1
Luque, I.2
Freire, E.3
-
27
-
-
33750040264
-
Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
-
Bussi G., Gervasio F., Laio A., and Parrinello M. Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics. J. Am. Chem. Soc. 128 (2006) 13435-13441
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 13435-13441
-
-
Bussi, G.1
Gervasio, F.2
Laio, A.3
Parrinello, M.4
-
28
-
-
0028710015
-
Local elevation: a method for improving the searching properties of molecular dynamics simulations
-
HÅber T., Torda A.E., and van Gunsteren W.F. Local elevation: a method for improving the searching properties of molecular dynamics simulations. J. Comput.-Aided Mol. Des. 8 (1994) 695-708
-
(1994)
J. Comput.-Aided Mol. Des.
, vol.8
, pp. 695-708
-
-
HÅber, T.1
Torda, A.E.2
van Gunsteren, W.F.3
-
29
-
-
0033556236
-
Peptide folding: when simulation meets experiment
-
Daura X., Gademann K., Jaun B., Seebach D., and van Gunsteren W.F. Peptide folding: when simulation meets experiment. Angew. Chem., Int. Ed. 38 (1999) 236-240
-
(1999)
Angew. Chem., Int. Ed.
, vol.38
, pp. 236-240
-
-
Daura, X.1
Gademann, K.2
Jaun, B.3
Seebach, D.4
van Gunsteren, W.F.5
-
30
-
-
17444412296
-
Assessing the accuracy of metadynamics
-
Laio A., Rodriguez-Fortea A., Gervasio F., Ceccarelli M., and Parrinello M. Assessing the accuracy of metadynamics. J. Phys. Chem. B 109 (2005) 6714-6721
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6714-6721
-
-
Laio, A.1
Rodriguez-Fortea, A.2
Gervasio, F.3
Ceccarelli, M.4
Parrinello, M.5
-
31
-
-
4143145167
-
10-residue folded peptide designed by segment statistics
-
Honda S., Yamasaki K., Sawada Y., and Morii H. 10-residue folded peptide designed by segment statistics. Structure 12 (2004) 1507-1518
-
(2004)
Structure
, vol.12
, pp. 1507-1518
-
-
Honda, S.1
Yamasaki, K.2
Sawada, Y.3
Morii, H.4
-
34
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins
-
Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G., Zhang W., et al. A point-charge force field for molecular mechanics simulations of proteins. J. Comput. Chem. 24 (2003) 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
-
35
-
-
0035425883
-
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
-
Schuler L.D., Daura X., and van Gunsteren W.F. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J. Comput. Chem. 22 (2001) 1205-1218
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 1205-1218
-
-
Schuler, L.D.1
Daura, X.2
van Gunsteren, W.F.3
-
36
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations
-
Kaminski G.A., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations. J. Phys. Chem. B 105 (2001) 6474-6487
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
37
-
-
0004067382
-
-
Reidel, Dordrecht, The Netherlands
-
Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Hermans J., and Pullman B. Intermolecular Forces (1981), Reidel, Dordrecht, The Netherlands
-
(1981)
Intermolecular Forces
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Hermans, J.4
Pullman, B.5
-
38
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory analysis
-
Lindhal E., Hess B., and van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7 (2001) 306-317
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindhal, E.1
Hess, B.2
van der Spoel, D.3
-
39
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essman U., Perera L., Berkowitz M.L., Darden T.A., Lee H., and Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essman, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.A.4
Lee, H.5
Pedersen, L.G.6
-
41
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics method
-
Nose S. A unified formulation of the constant temperature molecular dynamics method. J. Chem. Phys. 81 (1984) 511
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511
-
-
Nose, S.1
-
42
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H.J.C., Postma J.P.M., Van Gusteren W.F., DiNola A., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gusteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
43
-
-
0004016501
-
Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water
-
Jorgensen W.L., Chandrasekhar J., and Madura J.P. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J. Chem. Phys. 79 (1983) 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.P.3
|