-
5
-
-
0032053619
-
Simulations of protein folding and unfolding
-
Brooks C. Simulations of protein folding and unfolding. Curr Opin Struct Biol 1998;8:222-226.
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 222-226
-
-
Brooks, C.1
-
6
-
-
0028949547
-
Theoretical studies of protein folding and unfolding
-
Karplus M, Sali A. Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol 1995;5:58-73.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 58-73
-
-
Karplus, M.1
Sali, A.2
-
7
-
-
0031465967
-
New view of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis T, Karplus M. New view of protein folding reconciled with the old through multiple unfolding simulations. Science 1997;278:1928-1931.
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
8
-
-
0030939289
-
Molecular dynamics simulations of the unfolding of barnase in water and 8M aqueous urea
-
Tirado-Rives J, Orozco M, Jorgensen W. Molecular dynamics simulations of the unfolding of barnase in water and 8M aqueous urea. Biochemistry 1997;36:7313-7329.
-
(1997)
Biochemistry
, vol.36
, pp. 7313-7329
-
-
Tirado-Rives, J.1
Orozco, M.2
Jorgensen, W.3
-
9
-
-
0032555115
-
Synergy between simulation and experiment in describing the energy landscape of protein folding
-
Ladurner A, Itzhaki L, Daggett V, Fersht A. Synergy between simulation and experiment in describing the energy landscape of protein folding. Proc Natl Acad Sci USA 1998;95:8473-8478.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 8473-8478
-
-
Ladurner, A.1
Itzhaki, L.2
Daggett, V.3
Fersht, A.4
-
10
-
-
0032516205
-
The molecular elasticity of tenascin, an extracellular matrix protein
-
Oberhauser AF, Marszalek PE, Erickson H, Fernandez J. The molecular elasticity of tenascin, an extracellular matrix protein. Nature 1998;393:181-185.
-
(1998)
Nature
, vol.393
, pp. 181-185
-
-
Oberhauser, A.F.1
Marszalek, P.E.2
Erickson, H.3
Fernandez, J.4
-
11
-
-
0031767965
-
The mechanical stability of immunoglobulin and fibronectin III domains in the muscle protein titin measured by AFM
-
Rief M, Gautel M, Schemmel A, Gaub H. The mechanical stability of immunoglobulin and fibronectin III domains in the muscle protein titin measured by AFM. Biophys J 1998;75:3008-3014.
-
(1998)
Biophys J
, vol.75
, pp. 3008-3014
-
-
Rief, M.1
Gautel, M.2
Schemmel, A.3
Gaub, H.4
-
12
-
-
0031011695
-
Reversible unfolding of individual titin immunoglobulin domains by AFM
-
Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 1997;276:1109-1112.
-
(1997)
Science
, vol.276
, pp. 1109-1112
-
-
Rief, M.1
Gautel, M.2
Oesterhelt, F.3
Fernandez, J.M.4
Gaub, H.E.5
-
13
-
-
0033573912
-
Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch
-
Krammer A, Lu H, Isralewitz B, Schulten K, Vogel V. Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. Proc Natl Acad Sci USA 1999;96:1351-1356.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 1351-1356
-
-
Krammer, A.1
Lu, H.2
Isralewitz, B.3
Schulten, K.4
Vogel, V.5
-
14
-
-
0030982846
-
Connectin/titin, a giant elastic protein of muscle
-
Maruyama K. Connectin/titin, a giant elastic protein of muscle. FASEB J 1997;11:341-345.
-
(1997)
FASEB J
, vol.11
, pp. 341-345
-
-
Maruyama, K.1
-
15
-
-
0027172919
-
Mechanotransduction across the cell surface and through the cytoskeleton
-
Wang N, Butler JP, Ingber DE. Mechanotransduction across the cell surface and through the cytoskeleton. Science 1993;260:1124-1127.
-
(1993)
Science
, vol.260
, pp. 1124-1127
-
-
Wang, N.1
Butler, J.P.2
Ingber, D.E.3
-
16
-
-
0032550178
-
Human autoantibodies reveal titin as a chromosomal protein
-
Machado C, Sunkel CE, Andrew DJ. Human autoantibodies reveal titin as a chromosomal protein. J Cell Biol 1998;141:321-333.
-
(1998)
J Cell Biol
, vol.141
, pp. 321-333
-
-
Machado, C.1
Sunkel, C.E.2
Andrew, D.J.3
-
17
-
-
0031002460
-
Folding-unfolding transition in single titin modules characterized with laser tweezers
-
Kellermayer M, Smith S, Granzier H, Bustamante C. Folding-unfolding transition in single titin modules characterized with laser tweezers. Science 1997;276:1112-1116.
-
(1997)
Science
, vol.276
, pp. 1112-1116
-
-
Kellermayer, M.1
Smith, S.2
Granzier, H.3
Bustamante, C.4
-
18
-
-
0031006659
-
Elasticity and unfolding of single molecules of the giant protein titin
-
Tskhovrebova L, Trinick J, Sleep JA, Simmons RM. Elasticity and unfolding of single molecules of the giant protein titin. Nature 1997;387:308-312.
-
(1997)
Nature
, vol.387
, pp. 308-312
-
-
Tskhovrebova, L.1
Trinick, J.2
Sleep, J.A.3
Simmons, R.M.4
-
19
-
-
0002174423
-
Steered molecular dynamics
-
Deuflhard P, Hermans J, Leimkuhler B, et al., editors, Berlin: Springer-Verlag
-
Izrailev S, Stepaniants S, Isralewitz B, et al. Steered molecular dynamics. In: Deuflhard P, Hermans J, Leimkuhler B, et al., editors, Computational molecular dynamics: challenges, methods, ideas, Volume 4 of Lecture notes in computational science and engineering. Berlin: Springer-Verlag; 1998. p 36-62.
-
(1998)
Computational Molecular Dynamics: Challenges, Methods, Ideas, Volume 4 of Lecture Notes in Computational Science and Engineering
, vol.4
, pp. 36-62
-
-
Izrailev, S.1
Stepaniants, S.2
Isralewitz, B.3
-
20
-
-
0030378980
-
SMD: Visual steering of molecular dynamics for protein design
-
Leech J, Prins J, Hermans J. SMD: visual steering of molecular dynamics for protein design. IEEE Comp Sci Eng 1996;3:38-45.
-
(1996)
IEEE Comp Sci Eng
, vol.3
, pp. 38-45
-
-
Leech, J.1
Prins, J.2
Hermans, J.3
-
21
-
-
0030059225
-
Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force
-
Grubmüller H, Heymann B, Tavan P. Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force. Science 1996;271:997-999.
-
(1996)
Science
, vol.271
, pp. 997-999
-
-
Grubmüller, H.1
Heymann, B.2
Tavan, P.3
-
22
-
-
0030987036
-
Molecular dynamics study of unbinding of the avidin-biotin complex
-
Izrailev S, Stepaniants S, Balsera M, Oono Y, Schulten K. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J 1997;72:1568-1581.
-
(1997)
Biophys J
, vol.72
, pp. 1568-1581
-
-
Izrailev, S.1
Stepaniants, S.2
Balsera, M.3
Oono, Y.4
Schulten, K.5
-
23
-
-
0030834853
-
Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations
-
Isralewitz B, Izrailev S, Schulten K. Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations. Biophys J 1997;73:2972-2979.
-
(1997)
Biophys J
, vol.73
, pp. 2972-2979
-
-
Isralewitz, B.1
Izrailev, S.2
Schulten, K.3
-
24
-
-
0001068789
-
Extraction of lipids from phospholipid membranes by steered molecular dynamics
-
Stepaniants S, Izrailev S, Schulten K. Extraction of lipids from phospholipid membranes by steered molecular dynamics. J Mol Model 1997;3:473-475.
-
(1997)
J Mol Model
, vol.3
, pp. 473-475
-
-
Stepaniants, S.1
Izrailev, S.2
Schulten, K.3
-
25
-
-
0032906662
-
Unbinding of retinoic acid from its receptor studied by steered molecular dynamics
-
Kosztin D, Izrailev S, Schulten K. Unbinding of retinoic acid from its receptor studied by steered molecular dynamics. Biophys J 1999;76:188-197.
-
(1999)
Biophys J
, vol.76
, pp. 188-197
-
-
Kosztin, D.1
Izrailev, S.2
Schulten, K.3
-
26
-
-
0033136019
-
Investigating a back door mechanism of actin phosphate release by steered molecular dynamics
-
Wriggers W, Schulten K. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Proteins 1999;35:262-273.
-
(1999)
Proteins
, vol.35
, pp. 262-273
-
-
Wriggers, W.1
Schulten, K.2
-
27
-
-
0031848099
-
Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
-
Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J 1998;75:662-671.
-
(1998)
Biophys J
, vol.75
, pp. 662-671
-
-
Lu, H.1
Isralewitz, B.2
Krammer, A.3
Vogel, V.4
Schulten, K.5
-
28
-
-
0029980542
-
Structural basis of calcium-induced e-cadherin rigidification and dimerization
-
Nagar B, Overdulin M, Ikura M, Rini J. Structural basis of calcium-induced e-cadherin rigidification and dimerization. Nature 1996;380:360-364.
-
(1996)
Nature
, vol.380
, pp. 360-364
-
-
Nagar, B.1
Overdulin, M.2
Ikura, M.3
Rini, J.4
-
29
-
-
0029046132
-
The crystal structure of an n-terminal two-domain fragment of vascular cell adhesion molecule 1 (vcam-1)
-
Wang JH, Pepinsky RB, Stehle T, et al. The crystal structure of an n-terminal two-domain fragment of vascular cell adhesion molecule 1 (vcam-1). Proc Natl Acad Sci USA 1995;92:5714-5718.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 5714-5718
-
-
Wang, J.H.1
Pepinsky, R.B.2
Stehle, T.3
-
30
-
-
0030050396
-
2.0 angstroms crystal structure of a four-domain segment of human fibronectin encompassing the rgd loop and synergy region
-
Leahy DJ, Aukhil I, Erickson HP. 2.0 angstroms crystal structure of a four-domain segment of human fibronectin encompassing the rgd loop and synergy region. Cell 1996;84:155-164.
-
(1996)
Cell
, vol.84
, pp. 155-164
-
-
Leahy, D.J.1
Aukhil, I.2
Erickson, H.P.3
-
31
-
-
0029154240
-
The structure of chloroplast cytochrome c6 at 1.9 angstroms resolution: Evidence for functional oligomerization
-
Kerfeld C, Anwar H, Interrante R, Merchant S, Yeates T. The structure of chloroplast cytochrome c6 at 1.9 angstroms resolution: evidence for functional oligomerization. J Mol Biol 1996;250: 627.
-
(1996)
J Mol Biol
, vol.250
, pp. 627
-
-
Kerfeld, C.1
Anwar, H.2
Interrante, R.3
Merchant, S.4
Yeates, T.5
-
32
-
-
0026801084
-
Three-dimensional solution structure of the b domain of staphylococcal protein a: Comparisons of the solution and crystal structures
-
Gouda H, Torigoe H, Saito A, Sato M, Arata Y, Shimada I. Three-dimensional solution structure of the b domain of staphylococcal protein a: comparisons of the solution and crystal structures. Biochemistry 1992;31:9665-9672.
-
(1992)
Biochemistry
, vol.31
, pp. 9665-9672
-
-
Gouda, H.1
Torigoe, H.2
Saito, A.3
Sato, M.4
Arata, Y.5
Shimada, I.6
-
33
-
-
0028986240
-
Structure of the first C2 domain of synaptotagmin I: A novel Ca2+/phospholipid-binding fold
-
Brayn Sutton R, Davletov RA, Berghuis AM, Sudhof TC, Sprang SR. Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold. Cell 1995;80:929-938.
-
(1995)
Cell
, vol.80
, pp. 929-938
-
-
Brayn Sutton, R.1
Davletov, R.A.2
Berghuis, A.M.3
Sudhof, T.C.4
Sprang, S.R.5
-
34
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJ, et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
-
35
-
-
8344276781
-
NAMD - A parallel, object-oriented molecular dynamics program
-
Nelson M, Humphrey W, Gursoy A, et al. NAMD - A parallel, object-oriented molecular dynamics program. J Supercomputing App 1996;10:251-268.
-
(1996)
J Supercomputing App
, vol.10
, pp. 251-268
-
-
Nelson, M.1
Humphrey, W.2
Gursoy, A.3
-
36
-
-
0003769049
-
-
New Haven: The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University
-
Brünger AT. X-PLOR, Version 3.1: a system for x-ray crystallography and NMR. New Haven: The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University; 1992.
-
(1992)
X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR
-
-
Brünger, A.T.1
-
37
-
-
0041784950
-
All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field
-
MacKerell Jr AD, Bashford D, Bellott M, et al. All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field. J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell A.D., Jr.1
Bashford, D.2
Bellott, M.3
-
38
-
-
0030584660
-
Immunoglobulin-like modules from titin I-band: Extensible components of muscle elasticity
-
Improta S, Politou A, Pastore A. Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure 1996;4:323-337.
-
(1996)
Structure
, vol.4
, pp. 323-337
-
-
Improta, S.1
Politou, A.2
Pastore, A.3
-
39
-
-
0033616713
-
Mechanical and chemical unfolding of a single protein: A comparison
-
Carrion-Vazquez M, Oberhauser A, Fowler S, Marszalek P, Broedel S, Clarke J, Fernandez J. Mechanical and chemical unfolding of a single protein: a comparison. Proc Natl Acad Sci USA 1999;96:3694-3699.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3694-3699
-
-
Carrion-Vazquez, M.1
Oberhauser, A.2
Fowler, S.3
Marszalek, P.4
Broedel, S.5
Clarke, J.6
Fernandez, J.7
-
40
-
-
0032508555
-
The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin
-
Meekhof A, Hamill S, Arcus V, Clarke J, Freund S. The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin. J Mol Biol 1998;282:181-194.
-
(1998)
J Mol Biol
, vol.282
, pp. 181-194
-
-
Meekhof, A.1
Hamill, S.2
Arcus, V.3
Clarke, J.4
Freund, S.5
-
41
-
-
0030962748
-
Stretching single protein modules: Titin is a weird spring
-
Erickson H. Stretching single protein modules: titin is a weird spring. Science 1997;276:1090-1093.
-
(1997)
Science
, vol.276
, pp. 1090-1093
-
-
Erickson, H.1
-
42
-
-
0033445338
-
Steered molecular dynamics simulation of conformational changes of immunoglobulin domain 127 interprete atomic force microscopy observations
-
In press
-
Lu H, Schulten K. Steered molecular dynamics simulation of conformational changes of immunoglobulin domain 127 interprete atomic force microscopy observations. Chem Phys 1999: In press.
-
(1999)
Chem Phys
-
-
Lu, H.1
Schulten, K.2
-
43
-
-
0004043397
-
-
New York: Springer-Verlag
-
Hynes RO. Fibronectins. New York: Springer-Verlag; 1990.
-
(1990)
Fibronectins
-
-
Hynes, R.O.1
-
44
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution
-
Duan Y, Kollman P. Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution. Science 1998;282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.2
|