-
1
-
-
0037090781
-
Structure and mechanics of single biomolecules: Experiment and simulation
-
Lavery, R., A. Lebrun, J. F. Allemand, D. Bensimon, and V. Croquette. 2002. Structure and mechanics of single biomolecules: experiment and simulation. J. Phys. Condens. Matter. 14:R383-R414.
-
(2002)
J. Phys. Condens. Matter
, vol.14
-
-
Lavery, R.1
Lebrun, A.2
Allemand, J.F.3
Bensimon, D.4
Croquette, V.5
-
2
-
-
0038206538
-
Molecular nanosprings in spider capture-silk threads
-
Becker, N., E. Oroudjev, S. Mutz, J. P. Cleveland, P. K. Hansma, C. Y. Hayashi, D. E. Makarov, and H. G. Hansma. 2003. Molecular nanosprings in spider capture-silk threads. Nat. Mater. 2:278-283.
-
(2003)
Nat. Mater.
, vol.2
, pp. 278-283
-
-
Becker, N.1
Oroudjev, E.2
Mutz, S.3
Cleveland, J.P.4
Hansma, P.K.5
Hayashi, C.Y.6
Makarov, D.E.7
Hansma, H.G.8
-
3
-
-
0346668262
-
Force mode atomic force microscopy as a tool for protein folding studies
-
Best, R. B., D. J. Brockwell, J. L. Toca-Herrera, A. W. Blake, D. A. Smith, S. E. Radford, and J. Clarke. 2003. Force mode atomic force microscopy as a tool for protein folding studies. Anal. Chim. Acta. 479:87-105.
-
(2003)
Anal. Chim. Acta
, vol.479
, pp. 87-105
-
-
Best, R.B.1
Brockwell, D.J.2
Toca-Herrera, J.L.3
Blake, A.W.4
Smith, D.A.5
Radford, S.E.6
Clarke, J.7
-
4
-
-
0036280490
-
The effect of core destabilization on the mechanical resistance of I27
-
Brockwell, D. J., G. S. Beddard, J. Clarkson, R. C. Zinober, A. Blake, J. Trinick, P. D. Olmsted, D. A. Smith, and S. E. Radford. 2002. The effect of core destabilization on the mechanical resistance of I27. Biophys. J. 83:458-472.
-
(2002)
Biophys. J.
, vol.83
, pp. 458-472
-
-
Brockwell, D.J.1
Beddard, G.S.2
Clarkson, J.3
Zinober, R.C.4
Blake, A.5
Trinick, J.6
Olmsted, P.D.7
Smith, D.A.8
Radford, S.E.9
-
5
-
-
0033817704
-
Stretching single molecules into novel conformations using the atomic force microscope
-
Fisher, T. E., P. E. Marsalek, and J. M. Fernandez. 2000. Stretching single molecules into novel conformations using the atomic force microscope. Nat. Struct. Biol. 7:719-724.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 719-724
-
-
Fisher, T.E.1
Marsalek, P.E.2
Fernandez, J.M.3
-
6
-
-
0033214502
-
The study of protein mechanics with the atomic force microscope
-
Fisher, T. E., A. F. Oberhauser, M. C. Vezquez, P. E. Marsalek, and J. Fernandez. 1999. The study of protein mechanics with the atomic force microscope. Trends Biochem. Sci. 24:379-384.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 379-384
-
-
Fisher, T.E.1
Oberhauser, A.F.2
Vezquez, M.C.3
Marsalek, P.E.4
Fernandez, J.5
-
7
-
-
0034804341
-
Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation
-
Best, R. B., B. Li, A. Steward, V. Daggett, and J. Clarke. 2001. Can non-mechanical 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
-
8
-
-
0033523904
-
Mechanical unfolding intermediates in titin modules
-
Marszalek, P. E., H. Lu, H. Li, M. Carrion-Vazquez, A. F. Oberhauser, K. Schulten, and J. M. Fernandez. 1999. Mechanical unfolding intermediates in titin modules. Nature. 402:100-103.
-
(1999)
Nature
, vol.402
, pp. 100-103
-
-
Marszalek, P.E.1
Lu, H.2
Li, H.3
Carrion-Vazquez, M.4
Oberhauser, A.F.5
Schulten, K.6
Fernandez, J.M.7
-
9
-
-
0034081255
-
Mechanical unfolding of a beta-hairpin using molecular dynamics
-
Bryant, Z., V. S. Pande, and D. S. Rokhsar. 2000. Mechanical unfolding of a beta-hairpin using molecular dynamics. Biophys. J. 78:584-589.
-
(2000)
Biophys. J.
, vol.78
, pp. 584-589
-
-
Bryant, Z.1
Pande, V.S.2
Rokhsar, D.S.3
-
10
-
-
0031848099
-
Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
-
Lu, H., B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten. 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
-
11
-
-
0033445338
-
Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations
-
Lu, H., and K. Schulten. 1999. Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations. Chem. Phys. 247:141-153.
-
(1999)
Chem. Phys.
, vol.247
, pp. 141-153
-
-
Lu, H.1
Schulten, K.2
-
12
-
-
0037025564
-
Unfolding proteins under external forces: A solvable model under the self-consistent pair contact probability approximation
-
Shen, T., L. S. Canino, and J. A. McCammon. 2002. Unfolding proteins under external forces: a solvable model under the self-consistent pair contact probability approximation. Phys. Rev. Lett. 89:068103.
-
(2002)
Phys. Rev. Lett.
, vol.89
, pp. 068103
-
-
Shen, T.1
Canino, L.S.2
McCammon, J.A.3
-
13
-
-
0032988663
-
Strength of a weak bond connecting flexible polymer chains
-
Evans, E., and K. Ritchie. 1999. Strength of a weak bond connecting flexible polymer chains. Biophys. J. 76:2439-2447.
-
(1999)
Biophys. J.
, vol.76
, pp. 2439-2447
-
-
Evans, E.1
Ritchie, K.2
-
14
-
-
0042508740
-
The mechanical stability of ubiquitin is linkage dependent
-
Carrion-Vazques, M., H. Li, P. E. Marzalek, A. F. Oberhauser, and J. M. Fernandez. 2003. The mechanical stability of ubiquitin is linkage dependent. Nat. Struct. Biol. 10:738-743.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 738-743
-
-
Carrion-Vazques, M.1
Li, H.2
Marzalek, P.E.3
Oberhauser, A.F.4
Fernandez, J.M.5
-
15
-
-
0042508741
-
Pulling geometry defines the mechanical resistance of a β-sheet protein
-
Brockwell, D. J., E. Paci, R. C. Zinober, G. S. Beddard, P. D. Olmsted, D. A. Smith, R. N. Perham, and S. E. Radford. 2003. Pulling geometry defines the mechanical resistance of a β-sheet protein. Nat. Struct. Biol. 10:731-737.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 731-737
-
-
Brockwell, D.J.1
Paci, E.2
Zinober, R.C.3
Beddard, G.S.4
Olmsted, P.D.5
Smith, D.A.6
Perham, R.N.7
Radford, S.E.8
-
16
-
-
0035366858
-
Kinetic Monte Carlo simulation of titin unfolding
-
Makarov, D. E., P. K. Hansma, and H. Metiu. 2001. Kinetic Monte Carlo simulation of titin unfolding. J. Chem. Phys. 114:9663-9673.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 9663-9673
-
-
Makarov, D.E.1
Hansma, P.K.2
Metiu, H.3
-
17
-
-
4243754128
-
Nonequilibrium equality for free energy differences
-
Jarzynski, C. 1997. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78:2690-2693.
-
(1997)
Phys. Rev. Lett.
, vol.78
, pp. 2690-2693
-
-
Jarzynski, C.1
-
18
-
-
0035957335
-
How does a system respond when driven away from thermal equilibrium?
-
Jarzynski, C. 2001. How does a system respond when driven away from thermal equilibrium? Proc. Natl. Acad. Sci. USA. 98:3636-3638.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 3636-3638
-
-
Jarzynski, C.1
-
19
-
-
0035957434
-
From the cover: Free energy reconstruction from nonequilibrium single-molecule pulling experiments
-
Hummer, G., and A. Szabo. 2001. From the cover: free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc. Natl. Acad. Sci. USA. 98:3658-3661.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 3658-3661
-
-
Hummer, G.1
Szabo, A.2
-
20
-
-
0037036070
-
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's Equality
-
Liphardt, J., S. Dumont, S. B. Smith, I. Tinoco, and C. Bustamante. 2002. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's Equality. Science. 296:1832-1835.
-
(2002)
Science
, vol.296
, pp. 1832-1835
-
-
Liphardt, J.1
Dumont, S.2
Smith, S.B.3
Tinoco, I.4
Bustamante, C.5
-
21
-
-
0037109040
-
A two-state kinetic model for the unfolding of single molecules by mechanical force
-
Ritort, F., C. Bustamante, and I. Tinoco. 2002. A two-state kinetic model for the unfolding of single molecules by mechanical force. Proc. Natl. Acad. Sci. USA. 99:13544-13548.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 13544-13548
-
-
Ritort, F.1
Bustamante, C.2
Tinoco, I.3
-
22
-
-
24644450199
-
Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
-
Collin, D., F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco, Jr., and C. Bustamante. 2003. Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies. Nature. 437:231-234.
-
(2003)
Nature
, vol.437
, pp. 231-234
-
-
Collin, D.1
Ritort, F.2
Jarzynski, C.3
Smith, S.B.4
Tinoco Jr., I.5
Bustamante, C.6
-
23
-
-
0000765761
-
Entropy production fluctuation theorem and the nonequilibrium work relation for free-energy differences
-
Crooks, G. E. 1999. Entropy production fluctuation theorem and the nonequilibrium work relation for free-energy differences. Phys. Rev. E. 60:2721-2726.
-
(1999)
Phys. Rev. E
, vol.60
, pp. 2721-2726
-
-
Crooks, G.E.1
-
24
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
25
-
-
0000224283
-
CHARMM: The energy function and its parameterization with an overview of the program
-
P. v. R. Schleyer et al., editors. John Wiley & Sons, Chichester, UK
-
MacKerell, A. D., Jr., B. Brooks, C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus. 1998. CHARMM: The energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry, 1. P. v. R. Schleyer et al., editors. John Wiley & Sons, Chichester, UK. 271-277
-
(1998)
The Encyclopedia of Computational Chemistry
, vol.1
, pp. 271-277
-
-
MacKerell Jr., A.D.1
Brooks, B.2
Brooks III, C.L.3
Nilsson, L.4
Roux, B.5
Won, Y.6
Karplus, M.7
-
26
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein, F. C., T. F. Koetzle, G. J. Williams, E. F. Meyer, M. D. Brice, J. R. Rogers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1997. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
-
(1997)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
Meyer, E.F.4
Brice, M.D.5
Rogers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
27
-
-
0004016501
-
Comparison of simple potential function for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential function for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
28
-
-
0033917135
-
The key event in force-induced unfolding of titin's immunoglobulin domain
-
Lu, H., and K. Schulten. 2000. The key event in force-induced unfolding of titin's immunoglobulin domain. Biophys. J. 79:51-65.
-
(2000)
Biophys. J.
, vol.79
, pp. 51-65
-
-
Lu, H.1
Schulten, K.2
-
29
-
-
0002174423
-
Steered molecular dynamics
-
P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and R. D. Skeel, editors. Springer-Verlag, Berlin, Germany
-
Izrailev, S., S. Stepaniants, B. Isralewitz, D. Kosztin, H. Lu, F. Molnar, W. Wriggers, and K. Schulten. 1999. Steered molecular dynamics. In Computational Molecular Dynamics: Challenges, Methods, Ideas, Vol. 4 of Lecture Notes in Computational Science and Engineering. P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and R. D. Skeel, editors. Springer-Verlag, Berlin, Germany. 39-65.
-
(1999)
Computational Molecular Dynamics: Challenges, Methods, Ideas, Vol. 4 of Lecture Notes in Computational Science and Engineering
, vol.4
, pp. 39-65
-
-
Izrailev, S.1
Stepaniants, S.2
Isralewitz, B.3
Kosztin, D.4
Lu, H.5
Molnar, F.6
Wriggers, W.7
Schulten, K.8
-
30
-
-
0031011695
-
Reversible unfolding of individual titin immunoglobulin domains by AFM
-
Rief, M., M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub. 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
-
31
-
-
0034805058
-
Simulated refolding of stretched titin immunoglobulin domains
-
Gao, M., H. Lu, and K. Schulten. 2001. Simulated refolding of stretched titin immunoglobulin domains. Biophys. J. 81:2268-2277.
-
(2001)
Biophys. J.
, vol.81
, pp. 2268-2277
-
-
Gao, M.1
Lu, H.2
Schulten, K.3
|