-
1
-
-
0028335096
-
Structural mechanisms for domain movements in proteins
-
DOI 10.1021/bi00188a001
-
M. Gerstein, A.M. Lesk, and C. Chothia Structural mechanisms for domain movements in proteins Biochemistry 33 1994 6739 6749 (Pubitemid 24190795)
-
(1994)
Biochemistry
, vol.33
, Issue.22
, pp. 6739-6749
-
-
Gerstein, M.1
Lesk, A.M.2
Chothia, C.3
-
3
-
-
17044393884
-
Coarse-grained models for proteins
-
V. Tozzini Coarse-grained models for proteins Curr. Opin. Struct. Biol. 15 2005 144 150
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
4
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
DOI 10.1016/j.sbi.2004.03.009, PII S0959440X04000430
-
M. Feig, and C.L. Brooks 3rd Recent advances in the development and application of implicit solvent models in biomolecule simulations Curr. Opin. Struct. Biol. 14 2004 217 224 (Pubitemid 38495800)
-
(2004)
Current Opinion in Structural Biology
, vol.14
, Issue.2
, pp. 217-224
-
-
Feig, M.1
Brooks III, C.L.2
-
5
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
PII S0009261499011239
-
Y. Sugita, and Y. Okamoto Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 314 1999 141 151 (Pubitemid 129556751)
-
(1999)
Chemical Physics Letters
, vol.314
, Issue.1-2
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
6
-
-
0028710015
-
Local elevation: A method for improving the searching properties of molecular dynamics simulation
-
T. Huber, A.E. Torda, and W.F. van Gunsteren Local elevation: a method for improving the searching properties of molecular dynamics simulation J. Comput. Aided Mol. Des. 8 1994 695 708
-
(1994)
J. Comput. Aided Mol. Des.
, vol.8
, pp. 695-708
-
-
Huber, T.1
Torda, A.E.2
Van Gunsteren, W.F.3
-
7
-
-
0000689085
-
Predicting slow structural transitions in macromolecular systems: Conformational flooding
-
H. Grubmüller Predicting slow structural transitions in macromolecular systems: conformational flooding Phys. Rev. E 52 1995 2893 2906
-
(1995)
Phys. Rev. e
, vol.52
, pp. 2893-2906
-
-
Grubmüller, H.1
-
8
-
-
28844454252
-
Parallel tempering: Theory, applications, and new perspectives
-
DOI 10.1039/b509983h
-
D.J. Earl, and M.W. Deem Parallel tempering: theory, applications, and new perspectives Phys. Chem. Chem. Phys. 7 2005 3910 3916 (Pubitemid 41771858)
-
(2005)
Physical Chemistry Chemical Physics
, vol.7
, Issue.23
, pp. 3910-3916
-
-
Earl, D.J.1
Deem, M.W.2
-
11
-
-
72249090819
-
Fragment 101-108 of myelin oligodendrocyte glycoprotein: A possible lead compound for multiple sclerosis
-
C. Guardiani, and S. Marsili R. Livi Fragment 101-108 of myelin oligodendrocyte glycoprotein: a possible lead compound for multiple sclerosis J. Am. Chem. Soc. 131 2009 17176 17184
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 17176-17184
-
-
Guardiani, C.1
Marsili, S.2
Livi, R.3
-
13
-
-
3042801661
-
Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model
-
DOI 10.1002/prot.20104
-
A.K. Felts, and Y. Harano R.M. Levy Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model Proteins 56 2004 310 321 (Pubitemid 38850164)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.2
, pp. 310-321
-
-
Felts, A.K.1
Harano, Y.2
Gallicchio, E.3
Levy, R.M.4
-
14
-
-
0242322528
-
An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins
-
W. Im, M. Feig, and C.L. Brooks 3rd An implicit membrane Generalized Born theory for the study of structure, stability, and interactions of membrane proteins Biophys. J. 85 2003 2900 2918 (Pubitemid 37345782)
-
(2003)
Biophysical Journal
, vol.85
, Issue.5
, pp. 2900-2918
-
-
Im, W.1
Feig, M.2
Brooks III, C.L.3
-
16
-
-
4243661501
-
Constrained reaction coordinate dynamics for the simulation of rare events
-
E. Carter, and G. Ciccotti R. Kapral Constrained reaction coordinate dynamics for the simulation of rare events Chem. Phys. Lett. 156 1989 472 477
-
(1989)
Chem. Phys. Lett.
, vol.156
, pp. 472-477
-
-
Carter, E.1
Ciccotti, G.2
Kapral, R.3
-
18
-
-
17544365232
-
Finite temperature string method for the study of rare events
-
DOI 10.1021/jp0455430
-
E. Weinan, W. Ren, and E. Vanden-Eijnden Finite temperature string method for the study of rare events J. Phys. Chem. B 109 2005 6688 6693 (Pubitemid 40552536)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.14
, pp. 6688-6693
-
-
Weinan, E.1
Ren, W.2
Vanden-Eijnden, E.3
-
19
-
-
2942548219
-
Reconstructing the density of states by history-dependent metadynamics
-
C. Micheletti, A. Laio, and M. Parrinello Reconstructing the density of states by history-dependent metadynamics Phys. Rev. Lett. 92 2004 170601
-
(2004)
Phys. Rev. Lett.
, vol.92
, pp. 170601
-
-
Micheletti, C.1
Laio, A.2
Parrinello, M.3
-
20
-
-
0000309559
-
SWARM-MD: Searching conformational space by cooperative molecular dynamics
-
T. Huber, and W. van Gunsteren SWARM-MD: searching conformational space by cooperative molecular dynamics J. Phys. Chem. A 102 1998 5937 5943 (Pubitemid 128604897)
-
(1998)
Journal of Physical Chemistry A
, vol.102
, Issue.29
, pp. 5937-5943
-
-
Huber, T.1
Van Gunsteren, W.F.2
-
21
-
-
0036467163
-
Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics
-
DOI 10.1002/prot.1167
-
K.Y. Sanbonmatsu, and A.E. García Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics Proteins 46 2002 225 234 (Pubitemid 34052076)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.46
, Issue.2
, pp. 225-234
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
22
-
-
0023644679
-
Structure of ubiquitin refined at 1.8 resolution
-
S. Vijay-Kumar, C.E. Bugg, and W.J. Cook Structure of ubiquitin refined at 1.8 resolution J. Mol. Biol. 194 1987 531 544
-
(1987)
J. Mol. Biol.
, vol.194
, pp. 531-544
-
-
Vijay-Kumar, S.1
Bugg, C.E.2
Cook, W.J.3
-
23
-
-
0027006827
-
Conformational analysis of Met-enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multidimensional NMR and molecular modeling
-
W.H. Graham, E.S. Carter 2nd, and R.P. Hicks Conformational analysis of Met-enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multidimensional NMR and molecular modeling Biopolymers 32 1992 1755 1764
-
(1992)
Biopolymers
, vol.32
, pp. 1755-1764
-
-
Graham, W.H.1
Carter II, E.S.2
Hicks, R.P.3
-
24
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
DOI 10.1126/science.1157092
-
O.F. Lange, and N.A. Lakomek B.L. de Groot Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution Science 320 2008 1471 1475 (Pubitemid 351929422)
-
(2008)
Science
, vol.320
, Issue.5882
, pp. 1471-1475
-
-
Lange, O.F.1
Lakomek, N.-A.2
Fares, C.3
Schroder, G.F.4
Walter, K.F.A.5
Becker, S.6
Meiler, J.7
Grubmuller, H.8
Griesinger, C.9
De Groot, B.L.10
-
25
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
-
G. Torrie, and J. Valleau Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling J. Comput. Phys. 23 1977 187 199
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.1
Valleau, J.2
-
26
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
B. Brooks, and R. Bruccoleri M. Karplus CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Karplus, M.3
-
27
-
-
49349104659
-
Mechanism and energy landscape of domain swapping in the B1 domain of protein G
-
A. Malevanets, F.L. Sirota, and S.J. Wodak Mechanism and energy landscape of domain swapping in the B1 domain of protein G J. Mol. Biol. 382 2008 223 235
-
(2008)
J. Mol. Biol.
, vol.382
, pp. 223-235
-
-
Malevanets, A.1
Sirota, F.L.2
Wodak, S.J.3
-
29
-
-
33646650705
-
Reversible multiple time scale molecular dynamics
-
M. Tuckerman, B. Berne, and G. Martyna Reversible multiple time scale molecular dynamics J. Chem. Phys. 97 1992 1990 2001
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 1990-2001
-
-
Tuckerman, M.1
Berne, B.2
Martyna, G.3
-
30
-
-
21044449889
-
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
-
DOI 10.1002/prot.20408
-
A.J. Nederveen, and J.F. Doreleijers A.M. Bonvin RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank Proteins 59 2005 662 672 (Pubitemid 40695843)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 662-672
-
-
Nederveen, A.J.1
Doreleijers, J.F.2
Vranken, W.3
Miller, Z.4
Spronk, C.A.E.M.5
Nabuurs, S.B.6
Guntert, P.7
Livny, M.8
Markley, J.L.9
Nilges, M.10
Ulrich, E.L.11
Kaptein, R.12
Bonvin, A.M.J.J.13
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