-
1
-
-
0030059225
-
Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force
-
Grubmüller, H., Heymann, B., and Tavan, P. (1996) Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 271, 997– 999.
-
(1996)
Science
, vol.271
, pp. 997-999
-
-
Grubmüller, H.1
Heymann, B.2
Tavan, P.3
-
2
-
-
0030987036
-
Molecular dynamics study of unbinding of the avidin-biotin complex
-
Izrailev, S., Stepaniants, S., Balsera, M., Oono, Y., and Schulten, K. (1997) Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J. 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
-
3
-
-
0022114079
-
Protein states and protein quakes
-
Ansari, A., Berendzen, J., Browne, S. F., Frauenfelder, H., Iben, I. E. T., Sauke, T. B., Shyamsunder, E., and Young, R. D. (1985) Protein states and protein quakes. Proc. Natl. Acad. Sci. USA 82, 5000–5004.
-
(1985)
Proc. Natl. Acad. Sci. USA
, vol.82
, pp. 5000-5004
-
-
Ansari, A.1
Berendzen, J.2
Browne, S. F.3
Frauenfelder, H.4
Iben, I. E. T.5
Sauke, T. B.6
Shyamsunder, E.7
Young, R. D.8
-
4
-
-
0017258698
-
Single-channel currents recorded from membrane of denervated frog muscle fibres
-
Neher, E. and Sakmann, B. (1976) Single-channel currents recorded from membrane of denervated frog muscle fibres. Nature 260, 799–802.
-
(1976)
Nature
, vol.260
, pp. 799-802
-
-
Neher, E.1
Sakmann, B.2
-
6
-
-
0037026489
-
The voltage-gated potassium channels and their relatives
-
Yellen, G. (2002) The voltage-gated potassium channels and their relatives. Nature 419, 35–42.
-
(2002)
Nature
, vol.419
, pp. 35-42
-
-
Yellen, G.1
-
7
-
-
0023234106
-
Rebinding and relaxation in the myoglobin pocket
-
Ansari, A., Berendzen, J., Braunstein, D., Cowen, B. R., Frauenfelder, H., Hong, M. K., Iben, I. E. T., Johnson, J. B., Ormos, P., Sauke, T. B., Scholl, R., Schulte, A., Steinbach, P. J., Vittitow, J., and Young, R. D. (1987) Rebinding and relaxation in the myoglobin pocket. Biophys. Chem. 26, 337–355.
-
(1987)
Biophys. Chem
, vol.26
, pp. 337-355
-
-
Ansari, A.1
Berendzen, J.2
Braunstein, D.3
Cowen, B. R.4
Frauenfelder, H.5
Hong, M. K.6
Iben, I. E. T.7
Johnson, J. B.8
Ormos, P.9
Sauke, T. B.10
Scholl, R.11
Schulte, A.12
Steinbach, P. J.13
Vittitow, J.14
Young, R. D.15
-
8
-
-
0023140044
-
Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin
-
Elber, R. and Karplus, M. (1987) Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science 235, 318–321.
-
(1987)
Science
, vol.235
, pp. 318-321
-
-
Elber, R.1
Karplus, M.2
-
9
-
-
0030021471
-
Bio-molecular dynamics comes of age
-
Berendsen, H. J. C. (1996) Bio-molecular dynamics comes of age. Science 271, 954–955.
-
(1996)
Science
, vol.271
, pp. 954-955
-
-
Berendsen, H. J. C.1
-
10
-
-
0003530086
-
-
Los Alamos, LA
-
Fermi, E., Pasta, J., and Ulam, S. (1955) Studies in Nonlinear Problems, I. Los Alamos Report 1940, Los Alamos, LA .
-
(1955)
Studies in Nonlinear Problems, I. Los Alamos Report 1940
-
-
Fermi, E.1
Pasta, J.2
Ulam, S.3
-
11
-
-
0035861454
-
Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF
-
de Groot, B. L. and Grubmüller, H. (2001) Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF. Science 294, 2353–2357.
-
(2001)
Science
, vol.294
, pp. 2353-2357
-
-
de Groot, B. L.1
Grubmüller, H.2
-
12
-
-
0035812426
-
Simulation of the spontaneous aggregation of phospholipids into bilayers
-
Marrink, S. J., Lindahl, E., Edholm, O., and Mark, A. E. (2001) Simulation of the spontaneous aggregation of phospholipids into bilayers. J. Am. Chem. Soc. 123, 8638–8639.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 8638-8639
-
-
Marrink, S. J.1
Lindahl, E.2
Edholm, O.3
Mark, A. E.4
-
14
-
-
0036499409
-
Folding and stability of the three-stranded beta-sheet peptide betanova: insights from molecular dynamics simulations
-
Colombo, G., Roccatano, D., and Mark, A. E. (2002) Folding and stability of the three-stranded beta-sheet peptide betanova: insights from molecular dynamics simulations. Proteins 46, 380–392.
-
(2002)
Proteins
, vol.46
, pp. 380-392
-
-
Colombo, G.1
Roccatano, D.2
Mark, A. E.3
-
16
-
-
0017776823
-
Dynamics of folded proteins
-
McCammon, J. A., Gelin, B. R., and Karplus, M. (1977) Dynamics of folded proteins. Nature 267, 585–590.
-
(1977)
Nature
, vol.267
, pp. 585-590
-
-
McCammon, J. A.1
Gelin, B. R.2
Karplus, M.3
-
17
-
-
84946450438
-
Algorithms for macromolecular dynamics and constraint dynamics
-
van Gunsteren, W. F. and Berendsen, H. J. C. (1977) Algorithms for macromolecular dynamics and constraint dynamics. Molec. Phys. 34, 1311–1327.
-
(1977)
Molec. Phys
, vol.34
, pp. 1311-1327
-
-
van Gunsteren, W. F.1
Berendsen, H. J. C.2
-
18
-
-
0035861430
-
Reality simulation—observe while it happens
-
Berendsen, H. J. C. (2001) Reality simulation—observe while it happens. Science 294, 2304–2305.
-
(2001)
Science
, vol.294
, pp. 2304-2305
-
-
Berendsen, H. J. C.1
-
19
-
-
0035650033
-
Molecular dynamics simulation of biomolecular systems
-
van Gunsteren, W. F., Bakowies, D., Bürgi, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Glättli, A., Hansson, T., Oostenbrink, C., Peter, C., Pitera, J., Schuler, L., Soares, T., and Yu, H. (2001) Molecular dynamics simulation of biomolecular systems. Chimia 55, 856–860.
-
(2001)
Chimia
, vol.55
, pp. 856-860
-
-
van Gunsteren, W. F.1
Bakowies, D.2
Bürgi, R.3
Chandrasekhar, I.4
Christen, M.5
Daura, X.6
Gee, P.7
Glättli, A.8
Hansson, T.9
Oostenbrink, C.10
Peter, C.11
Pitera, J.12
Schuler, L.13
Soares, T.14
Yu, H.15
-
21
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M. and McCammon, J. A. (2002) Molecular dynamics simulations of biomolecules. Nature Struct. Biol. 9, 646–652.
-
(2002)
Nature Struct. Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J. A.2
-
22
-
-
76549252207
-
The structure of proteins: two hydrogen-bonded helical configurations of polypeptide chain
-
Pauling, L., Corey, R. B., and Branson, H. R. (1951) The structure of proteins: two hydrogen-bonded helical configurations of polypeptide chain. Proc. Natl. Acad. Sci. USA 37, 205.
-
(1951)
Proc. Natl. Acad. Sci. USA
, vol.37
, pp. 205
-
-
Pauling, L.1
Corey, R. B.2
Branson, H. R.3
-
24
-
-
2142813682
-
Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry
-
van Gunsteren, W. F. and Berendsen, H. J. C. (1990) Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. 29, 992–1023.
-
(1990)
Angew. Chem. Int. Ed
, vol.29
, pp. 992-1023
-
-
van Gunsteren, W. F.1
Berendsen, H. J. C.2
-
25
-
-
0001994422
-
Simulating complex systems without adjustable parameters
-
Parrinello, M. (2000) Simulating complex systems without adjustable parameters. IEEE Comput. Sci. Eng. 2, 22–27.
-
(2000)
IEEE Comput. Sci. Eng
, vol.2
, pp. 22-27
-
-
Parrinello, M.1
-
26
-
-
0000695782
-
Understanding modern molecular dynamics: techniques and applications
-
Tuckerman, M. E. and Martyna, G. J. (2000) Understanding modern molecular dynamics: techniques and applications. J. Phys. Chem. B. 104, 159–178.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 159-178
-
-
Tuckerman, M. E.1
Martyna, G. J.2
-
27
-
-
0003475941
-
-
eds. (–1997) Escom, Leiden, The Netherlands
-
van Gunsteren, W. F., Weiner, P. K., and Wilkinson, A. J., eds. (1989–1997) Computer Simulation of Biomolecular Systems: Theoretical and Experimiental Applications, vol. 1–3, Escom, Leiden, The Netherlands.
-
(1989)
Computer Simulation of Biomolecular Systems: Theoretical and Experimiental Applications, vol. 1–3
-
-
van Gunsteren, W. F.1
Weiner, P. K.2
Wilkinson, A. J.3
-
28
-
-
0012618901
-
Atomic force microscope
-
Binnig, G., Quate, C. F., and Gerber, C. H. (1986) Atomic force microscope. Phys. Rev. Lett. 56, 930–933.
-
(1986)
Phys. Rev. Lett
, vol.56
, pp. 930-933
-
-
Binnig, G.1
Quate, C. F.2
Gerber, C. H.3
-
29
-
-
0028309424
-
Adhesion forces between individual ligand-receptor pairs
-
Florin, E.-L., Moy, V. T., and Gaub, H. E. (1994) Adhesion forces between individual ligand-receptor pairs. Science 264, 415–417.
-
(1994)
Science
, vol.264
, pp. 415-417
-
-
Florin, E.-L.1
Moy, V. T.2
Gaub, H. E.3
-
30
-
-
0028381539
-
Sensing discrete streptavidin-biotin interactions with atomic force microscopy
-
Lee, G. U., Kidwell, D. A., and Colton, R. J. (1994) Sensing discrete streptavidin-biotin interactions with atomic force microscopy. Langmuir 10, 354–357.
-
(1994)
Langmuir
, vol.10
, pp. 354-357
-
-
Lee, G. U.1
Kidwell, D. A.2
Colton, R. J.3
-
31
-
-
0028261701
-
Single myosin molecule mechanics: piconewton forces and nanometer steps
-
Finer, J. T., Simmons, R. M., and Spudich, J. A. (1994) Single myosin molecule mechanics: piconewton forces and nanometer steps. Nature 368, 113–119.
-
(1994)
Nature
, vol.368
, pp. 113-119
-
-
Finer, J. T.1
Simmons, R. M.2
Spudich, J. A.3
-
32
-
-
0029416931
-
Transcription against an applied force
-
Yin, H., Wang, M. D., Svoboda, K., Landick, R., Block, S. M., and Gelles, J. (1995) Transcription against an applied force. Science 270, 1653–1657.
-
(1995)
Science
, vol.270
, pp. 1653-1657
-
-
Yin, H.1
Wang, M. D.2
Svoboda, K.3
Landick, R.4
Block, S. M.5
Gelles, J.6
-
33
-
-
0000689085
-
Predicting slow structural transitions in macromolecular systems: conformational flooding
-
Grubmüller, H. (1995) Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys. Rev. E. 52, 2893.
-
(1995)
Phys. Rev. E
, vol.52
, pp. 2893
-
-
Grubmüller, H.1
-
34
-
-
0037080723
-
Predicting unimolecular chemical reactions: Chemical flooding
-
Müller, E. M., de Meijere, A., and Grubmüller, H. (2002) Predicting unimolecular chemical reactions: Chemical flooding. Biophys. J. 116, 897–905.
-
(2002)
Biophys. J
, vol.116
, pp. 897-905
-
-
Müller, E. M.1
de Meijere, A.2
Grubmüller, H.3
-
35
-
-
0031011695
-
Reversible unfolding of individual titin immunoglobulin domains by AFM
-
Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J. M., and Gaub, H. E. (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 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
-
36
-
-
0033616713
-
Mechanical and chemical unfolding of a single protein: A comparison
-
Carrion-Vazquez, M., Oberhauser, A. F., Fowler, S. B., Marszalek, P. E., Broedel, S. E., Clarke, J., and Fernandez, J. M. (1999) Mechanical and chemical unfolding of a single protein: A comparison. Proc. Natl. Acad. Sci. USA 96, 3694–3699.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 3694-3699
-
-
Carrion-Vazquez, M.1
Oberhauser, A. F.2
Fowler, S. B.3
Marszalek, P. E.4
Broedel, S. E.5
Clarke, J.6
Fernandez, J. M.7
-
37
-
-
0037066262
-
Force spectroscopy of single biomolecules
-
Rief, M. and Grubmüller, H. (2002) Force spectroscopy of single biomolecules. Chem. Phys. Chem. 3, 255–261.
-
(2002)
Chem. Phys. Chem
, vol.3
, pp. 255-261
-
-
Rief, M.1
Grubmüller, H.2
-
38
-
-
0031848099
-
Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
-
Lu, H., Isralewitz, B., Krammer, A., Vogel, V., and Schulten, K. (1998) Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 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
-
39
-
-
0033523904
-
Mechanical unfolding intermediates in titin modules
-
Marszalek, P., Lu, H., Li, H., Carrion-Vazquez, M., Oberhauser, A. F., Schulten, K., and Fernandez, J. M. (1999) Mechanical unfolding intermediates in titin modules. Nature 402, 100–103.
-
(1999)
Nature
, vol.402
, pp. 100-103
-
-
Marszalek, P.1
Lu, H.2
Li, H.3
Carrion-Vazquez, M.4
Oberhauser, A. F.5
Schulten, K.6
Fernandez, J. M.7
-
40
-
-
0033531973
-
Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations
-
Paci, E. and Karplus, M. (1999) Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J. Molec. Biol. 288, 441–459.
-
(1999)
J. Molec. Biol
, vol.288
, pp. 441-459
-
-
Paci, E.1
Karplus, M.2
-
41
-
-
0033917135
-
The key event in force-induced unfolding of titin’s immunoglubin domains
-
Lu, H. and Schulten, K. (2000) The key event in force-induced unfolding of titin’s immunoglubin domains. Biophys. J. 79, 51–65.
-
(2000)
Biophys. J
, vol.79
, pp. 51-65
-
-
Lu, H.1
Schulten, K.2
-
42
-
-
0034804341
-
Can non-me-chanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation
-
Best, R. B., Li, B., Steward, A., Daggett, V., and Clarke, J. (2001) Can non-me-chanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys. J. 81, 2344–2356.
-
(2001)
Biophys. J
, vol.81
, pp. 2344-2356
-
-
Best, R. B.1
Li, B.2
Steward, A.3
Daggett, V.4
Clarke, J.5
-
43
-
-
0035976752
-
Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study
-
Paci, E., Caflisch, A., Plückthun, A., and Karplus, M. (2001) Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. J. Molec. Biol. 314, 589–605.
-
(2001)
J. Molec. Biol
, vol.314
, pp. 589-605
-
-
Paci, E.1
Caflisch, A.2
Plückthun, A.3
Karplus, M.4
-
44
-
-
0036389817
-
Mechanical unfolding of a titin Ig domain: Structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering
-
Fowlere, S. B., Best, R. B., Herrera, J. L. T., Rutherford, T. J., Steward, A., Paci, E., Karplus, M., and Clarke, J. (2002) Mechanical unfolding of a titin Ig domain: Structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J. Mol. Biol. 322, 841–849.
-
(2002)
J. Mol. Biol
, vol.322
, pp. 841-849
-
-
Fowlere, S. B.1
Best, R. B.2
Herrera, J. L. T.3
Rutherford, T. J.4
Steward, A.5
Paci, E.6
Karplus, M.7
Clarke, J.8
-
45
-
-
0031042739
-
Single molecule force spectroscopy reveals conformational change in polysaccharides
-
Rief, M., Oesterhelt, F., Heymann, B., and Gaub, H. E. (1997) Single molecule force spectroscopy reveals conformational change in polysaccharides. Science 275, 1295–1297.
-
(1997)
Science
, vol.275
, pp. 1295-1297
-
-
Rief, M.1
Oesterhelt, F.2
Heymann, B.3
Gaub, H. E.4
-
46
-
-
0344327079
-
Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads
-
MacKerell, A. D. and Lee, G. U. (1999) Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads. Europ. Biophys. J. 28, 415–426.
-
(1999)
Europ. Biophys. J
, vol.28
, pp. 415-426
-
-
MacKerell, A. D.1
Lee, G. U.2
-
47
-
-
0002688989
-
Elastic properties of poly(ethylene-gly-col) studied by molecular dynamics stretching simulations
-
Heymann, B. and Grubmüller, H. (1999) Elastic properties of poly(ethylene-gly-col) studied by molecular dynamics stretching simulations. Chem. Phys. Lett. 307, 425–432.
-
(1999)
Chem. Phys. Lett
, vol.307
, pp. 425-432
-
-
Heymann, B.1
Grubmüller, H.2
-
48
-
-
0042852135
-
Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations
-
Gullingsrud, J., Braun, R., and Schulten, K. (1999) Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J. Comp. Phys. 151, 190–211.
-
(1999)
J. Comp. Phys
, vol.151
, pp. 190-211
-
-
Gullingsrud, J.1
Braun, R.2
Schulten, K.3
-
49
-
-
0042885340
-
Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality
-
Park, S., Khalili-Araghi, F., Tajkhorshid, E., and Schulten, K. (2003) Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality. J. Chem. Phys. 119, 3559–3566.
-
(2003)
J. Chem. Phys
, vol.119
, pp. 3559-3566
-
-
Park, S.1
Khalili-Araghi, F.2
Tajkhorshid, E.3
Schulten, K.4
-
50
-
-
4143087050
-
Calculating potentials of mean force from steered molecular dynamics simulations
-
Park, S. and Schulten, K. (2004) Calculating potentials of mean force from steered molecular dynamics simulations. J. Chem. Phys. 120, 5946–5961.
-
(2004)
J. Chem. Phys
, vol.120
, pp. 5946-5961
-
-
Park, S.1
Schulten, K.2
-
51
-
-
0035312645
-
Steered molecular dynamics and mechanical functions of proteins
-
Isralewitz, B., Gao, M., and Schulten, K. (2001) Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11, 224–230.
-
(2001)
Curr. Opin. Struct. Biol
, vol.11
, pp. 224-230
-
-
Isralewitz, B.1
Gao, M.2
Schulten, K.3
-
52
-
-
1442328108
-
Advances in biomolecular simulations: methodology and recent applications
-
Norberg, J. and Nilsson, L. (2003) Advances in biomolecular simulations: methodology and recent applications. Q. Rev. Biophys. 36, 257–306.
-
(2003)
Q. Rev. Biophys
, vol.36
, pp. 257-306
-
-
Norberg, J.1
Nilsson, L.2
-
53
-
-
0018101150
-
Models for specific adhesion of cells to cells
-
Bell, G. I. (1978) Models for specific adhesion of cells to cells. Science 200, 618–627.
-
(1978)
Science
, vol.200
, pp. 618-627
-
-
Bell, G. I.1
-
54
-
-
0031001349
-
Dynamic strength of molecular adhesion bonds
-
Evans, E. and Ritchie, K. (1997) Dynamic strength of molecular adhesion bonds. Biophys. J. 72, 1541–1555.
-
(1997)
Biophys. J
, vol.72
, pp. 1541-1555
-
-
Evans, E.1
Ritchie, K.2
-
55
-
-
0034688856
-
Rupture of multiple parallel molecular bonds under dynamic loading
-
Seifert, U. (2000) Rupture of multiple parallel molecular bonds under dynamic loading. Phys. Rev. Lett. 84, 2750–2753.
-
(2000)
Phys. Rev. Lett
, vol.84
, pp. 2750-2753
-
-
Seifert, U.1
-
56
-
-
0342350248
-
Dynamic force spectroscopy of molecular adhesion bonds
-
Heymann, B. and Grubmüller, H. (2000) Dynamic force spectroscopy of molecular adhesion bonds. Phys. Rev. Lett. 84, 6126–6129.
-
(2000)
Phys. Rev. Lett
, vol.84
, pp. 6126-6129
-
-
Heymann, B.1
Grubmüller, H.2
-
57
-
-
0038650860
-
Kinetics from nonequilibrium single-molecule pulling experiments
-
Hummer, G. and Szabo, A. (2003) Kinetics from nonequilibrium single-molecule pulling experiments. Biophys. J. 85, 5–15.
-
(2003)
Biophys. J
, vol.85
, pp. 5-15
-
-
Hummer, G.1
Szabo, A.2
-
58
-
-
2142746284
-
The activated complex in chemical reactions
-
Eyring, H. (1935) The activated complex in chemical reactions. J. Chem. Phys. 3, 107–115.
-
(1935)
J. Chem. Phys
, vol.3
, pp. 107-115
-
-
Eyring, H.1
-
59
-
-
34547275473
-
Brownian motion in a field of force and the diffusion model of chemical reactions
-
Kramers, H. A. (1940) Brownian motion in a field of force and the diffusion model of chemical reactions. Physica (Utrecht) VII, 284–304.
-
(1940)
Physica (Utrecht)
, vol.VII
, pp. 284-304
-
-
Kramers, H. A.1
-
60
-
-
0347193736
-
Reaction-rate theory: fifty years after Kramers
-
Hänggi, P., Talkner, P., and Borkovec, M. (1990) Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62, 251–341.
-
(1990)
Rev. Mod. Phys
, vol.62
, pp. 251-341
-
-
Hänggi, P.1
Talkner, P.2
Borkovec, M.3
-
61
-
-
0013412734
-
AN02/DNP unbinding forces studied by molecular dynamics AFM simulations
-
Heymann, B. and Grubmüller, H. (1999) AN02/DNP unbinding forces studied by molecular dynamics AFM simulations. Chem. Phys. Lett. 303, 1–9.
-
(1999)
Chem. Phys. Lett
, vol.303
, pp. 1-9
-
-
Heymann, B.1
Grubmüller, H.2
-
62
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory analysis
-
Lindahl, E., Hess, B., and van der Spoel, D. (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7, 306–317.
-
(2001)
J. Mol. Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
63
-
-
85194662319
-
-
Technical report, Beckman Institute
-
Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kalé, L., Skeel, R. D., and Schulten, K. (1995) NAMD–a parallel, object-oriented molecular dynamics program. Technical report, Beckman Institute.
-
(1995)
NAMD–a parallel, object-oriented molecular dynamics program
-
-
Nelson, M.1
Humphrey, W.2
Gursoy, A.3
Dalke, A.4
Kalé, L.5
Skeel, R. D.6
Schulten, K.7
-
64
-
-
0001464448
-
EGO—An efficient molecular dynamics program and its application to protein dynamics simulations
-
(Esser, R., Grassberger, P., Grotendorst, J., and Lewerenz, M., eds), World Scientific, Singapore 912805
-
Eichinger, M., Heller, H., and Grubmüller, H. (2000) EGO—An efficient molecular dynamics program and its application to protein dynamics simulations, in: Workshop on Molecular Dynamics on Parallel Computers, John von Neumann Institute for Computing (NIC) Research Centre Jülich, Germany, 8–10 February 1999, (Esser, R., Grassberger, P., Grotendorst, J., and Lewerenz, M., eds.), pp. 154–174, World Scientific, Singapore 912805.
-
(2000)
Workshop on Molecular Dynamics on Parallel Computers, John von Neumann Institute for Computing (NIC) Research Centre Jülich, Germany, 8–10 February 1999
, pp. 154-174
-
-
Eichinger, M.1
Heller, H.2
Grubmüller, H.3
-
65
-
-
0033954256
-
The protein data bank
-
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The protein data bank. Nucleic Acids Res. 28, 235–242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H. M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T. N.5
Weissig, H.6
Shindyalov, I. N.7
Bourne, P. E.8
-
67
-
-
0028071373
-
Entropic elasticity of lambda-phage DNA
-
Bustamante, C., Marko, J. F., Siggia, E. D., and Smith, S. (1994) Entropic elasticity of lambda-phage DNA. Science 265, 1599–1600.
-
(1994)
Science
, vol.265
, pp. 1599-1600
-
-
Bustamante, C.1
Marko, J. F.2
Siggia, E. D.3
Smith, S.4
-
68
-
-
0034500645
-
Similarities between principal components of protein dynamics and random diffusion
-
Hess, B. (2000) Similarities between principal components of protein dynamics and random diffusion. Phys. Rev. E. 62, 8438–8448.
-
(2000)
Phys. Rev. E
, vol.62
, pp. 8438-8448
-
-
Hess, B.1
-
69
-
-
0032584783
-
Reversible peptide folding in solution by molecular dynamics simulation
-
Daura, X., Jaun, B., Seebach, D., van Gunsteren, W. F., and Mark, A. E. (1998) Reversible peptide folding in solution by molecular dynamics simulation. J. Molec. Biol. 280, 925–932.
-
(1998)
J. Molec. Biol
, vol.280
, pp. 925-932
-
-
Daura, X.1
Jaun, B.2
Seebach, D.3
van Gunsteren, W. F.4
Mark, A. E.5
-
70
-
-
0033557181
-
Folding-unfolding thermodynamics of a β-heptapeptide from eqilibrium simulations
-
Daura, X., van Gunsteren, W. F., and Mark, A. E. (1999) Folding-unfolding thermodynamics of a β-heptapeptide from eqilibrium simulations. Proteins: Structure, Function, and Genetics 34, 269–280.
-
(1999)
Proteins: Structure, Function, and Genetics
, vol.34
, pp. 269-280
-
-
Daura, X.1
van Gunsteren, W. F.2
Mark, A. E.3
-
71
-
-
0034825161
-
A strategy for analysis of (molecular) equilibrium simulations: configuration space density estimation, clustering, and visualization
-
Hamprecht, F. A., Peter, C., Daura, X., Thiel, W., and van Gunsteren, W. F. (2001) A strategy for analysis of (molecular) equilibrium simulations: configuration space density estimation, clustering, and visualization. J. Chem. Phys. 114, 2079–2089.
-
(2001)
J. Chem. Phys
, vol.114
, pp. 2079-2089
-
-
Hamprecht, F. A.1
Peter, C.2
Daura, X.3
Thiel, W.4
van Gunsteren, W. F.5
-
72
-
-
0035946983
-
Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds
-
de Groot, B. L., Daura, X., Mark, A. E., and Grubmüller, H. (2001) Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. J. Molec. Biol. 309, 299–313.
-
(2001)
J. Molec. Biol
, vol.309
, pp. 299-313
-
-
de Groot, B. L.1
Daura, X.2
Mark, A. E.3
Grubmüller, H.4
-
73
-
-
0037103003
-
Assessing equilibration and convergence in biomolecular simulations
-
X. D., and
-
L.J. Smith, X. D., and van Gunsteren, W. (2002) Assessing equilibration and convergence in biomolecular simulations. Proteins 48, 487–496.
-
(2002)
Proteins
, vol.48
, pp. 487-496
-
-
Smith, L.J.1
van Gunsteren, W.2
-
74
-
-
0041305824
-
Structural transitions and elasticity from torque measurements on DNA
-
Bryant, Z., Stone, M. D., Gore, J., Smith, S. B., Cozzarelli, N. R., and Bustamante, C. (2003) Structural transitions and elasticity from torque measurements on DNA. Nature 424, 338–341.
-
(2003)
Nature
, vol.424
, pp. 338-341
-
-
Bryant, Z.1
Stone, M. D.2
Gore, J.3
Smith, S. B.4
Cozzarelli, N. R.5
Bustamante, C.6
-
75
-
-
0034874258
-
Molecular dynamics force probe simulations of antibody/antigen unbinding: entropic control and non-additivity of unbinding forces
-
Heymann, B. and Grubmüller, H. (2001) Molecular dynamics force probe simulations of antibody/antigen unbinding: entropic control and non-additivity of unbinding forces. Biophys. J. 81, 1295–1313.
-
(2001)
Biophys. J
, vol.81
, pp. 1295-1313
-
-
Heymann, B.1
Grubmüller, H.2
|