-
1
-
-
78651189765
-
On the nature of allosteric transitions: a plausible model
-
Monod J., Wyman J., and Changeux J.P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12 (1965) 88-118
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
2
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman K., and Kern D. Dynamic personalities of proteins. Nature 450 (2007) 964-972
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
3
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern D., and Zuiderweg E.R.P. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13 (2003) 748-757
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.R.P.2
-
4
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder H., Sligar S.G., and Wolynes P.G. The energy landscapes and motions of proteins. Science 254 (1991) 1598-1603
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
5
-
-
0033970020
-
Folding and binding cascades: dynamic landscapes and population shifts
-
Kumar S., Ma B., Tsai C.J., Sinha N., and Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9 (2000) 10-19
-
(2000)
Protein Sci.
, vol.9
, pp. 10-19
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Sinha, N.4
Nussinov, R.5
-
6
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations
-
Ma B., Shatsky M., Wolfson H.J., and Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11 (2002) 184-197
-
(2002)
Protein Sci.
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
7
-
-
48249141040
-
Allostery and cooperativity revisited
-
Cui Q., and Karplus M. Allostery and cooperativity revisited. Protein Sci. 17 (2008) 1295-1307
-
(2008)
Protein Sci.
, vol.17
, pp. 1295-1307
-
-
Cui, Q.1
Karplus, M.2
-
10
-
-
25444469141
-
Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen
-
Kazmirski S.L., Zhao Y.X., Bowman G.D., O'Donnell M., and Kuriyan J. Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen. Proc. Natl Acad. Sci. USA 102 (2005) 13801-13806
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 13801-13806
-
-
Kazmirski, S.L.1
Zhao, Y.X.2
Bowman, G.D.3
O'Donnell, M.4
Kuriyan, J.5
-
11
-
-
0028455053
-
Targeted molecular dynamics: a new approach for searching pathways of conformational transitions
-
Schlitter J., Engels M., and Kruger P. Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J. Mol. Graphics 12 (1994) 84-89
-
(1994)
J. Mol. Graphics
, vol.12
, pp. 84-89
-
-
Schlitter, J.1
Engels, M.2
Kruger, P.3
-
12
-
-
0000689085
-
Predicting slow structural transitions in macromolecular systems: conformational flooding
-
Grubmüller H. 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
-
13
-
-
4344606960
-
Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations
-
Bartels C., and Karplus M. Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations. J. Comput. Chem. 18 (1997) 1450-1462
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1450-1462
-
-
Bartels, C.1
Karplus, M.2
-
14
-
-
0030711616
-
Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21
-
Ma J., and Karplus M. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proc. Natl Acad. Sci. USA 94 (1997) 11905
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 11905
-
-
Ma, J.1
Karplus, M.2
-
15
-
-
0036424048
-
Transition path sampling: throwing ropes over rough mountain passes, in the dark
-
Bolhuis P.G., Chandler D., Dellago C., and Geissler P.L. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53 (2002) 291-318
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
17
-
-
14844286108
-
Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
-
Ma J. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13 (2005) 373-380
-
(2005)
Structure
, vol.13
, pp. 373-380
-
-
Ma, J.1
-
18
-
-
33747065536
-
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations
-
Okazaki K., Koga N., Takada S., Onuchic J.N., and Wolynes P.G. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations. Proc. Natl Acad. Sci. USA 103 (2006) 11844
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 11844
-
-
Okazaki, K.1
Koga, N.2
Takada, S.3
Onuchic, J.N.4
Wolynes, P.G.5
-
19
-
-
33748253737
-
Simulation of conformational transitions
-
van der Vaart A. Simulation of conformational transitions. Theor. Chem. Acc. 116 (2006) 183-193
-
(2006)
Theor. Chem. Acc.
, vol.116
, pp. 183-193
-
-
van der Vaart, A.1
-
20
-
-
37649014404
-
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: a review
-
Christen M., and van Gunsteren W.F. On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: a review. J. Comput. Chem. 29 (2008) 157-166
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 157-166
-
-
Christen, M.1
van Gunsteren, W.F.2
-
21
-
-
41949100049
-
Recent advances in implicit solvent-based methods for biomolecular simulations
-
Chen J., Brooks C.L., and Khandogin J. Recent advances in implicit solvent-based methods for biomolecular simulations. Curr. Opin. Struct. Biol. 18 (2008) 140-148
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 140-148
-
-
Chen, J.1
Brooks, C.L.2
Khandogin, J.3
-
22
-
-
0027794972
-
Targeted molecular dynamics simulation of conformational change-application to the T ↔ R transition in insulin
-
Schlitter J., Engels M., Krüger P., Jacoby E., and Wollmer A. Targeted molecular dynamics simulation of conformational change-application to the T ↔ R transition in insulin. Mol. Simul. 10 (1993) 291-308
-
(1993)
Mol. Simul.
, vol.10
, pp. 291-308
-
-
Schlitter, J.1
Engels, M.2
Krüger, P.3
Jacoby, E.4
Wollmer, A.5
-
23
-
-
0000127140
-
Method for estimating the configurational entropy of macromolecules
-
Karplus M., and Kushick J.N. Method for estimating the configurational entropy of macromolecules. Macromolecules 14 (1981) 325-332
-
(1981)
Macromolecules
, vol.14
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.N.2
-
24
-
-
0026076090
-
Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
-
Ichiye T., and Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins Struct. Funct. Genet. 11 (1991) 205-217
-
(1991)
Proteins Struct. Funct. Genet.
, vol.11
, pp. 205-217
-
-
Ichiye, T.1
Karplus, M.2
-
26
-
-
0020698476
-
Dynamics of proteins: elements and function
-
Karplus M., and McCammon J.A. Dynamics of proteins: elements and function. Annu. Rev. Biochem. 52 (1983) 263-300
-
(1983)
Annu. Rev. Biochem.
, vol.52
, pp. 263-300
-
-
Karplus, M.1
McCammon, J.A.2
-
27
-
-
0001295503
-
Principal component analysis and long time protein dynamics
-
Balsera M.A., Wriggers W., Oono Y., and Schulten K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100 (1996) 2567-2572
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2567-2572
-
-
Balsera, M.A.1
Wriggers, W.2
Oono, Y.3
Schulten, K.4
-
28
-
-
0000118827
-
Harmonic and quasiharmonic descriptions of crambin
-
Teeter M.M., and Case D.A. Harmonic and quasiharmonic descriptions of crambin. J. Phys. Chem. 194 (1990) 8091-8097
-
(1990)
J. Phys. Chem.
, vol.194
, pp. 8091-8097
-
-
Teeter, M.M.1
Case, D.A.2
-
29
-
-
0242618314
-
Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum
-
Díaz J.F., Wroblowski B., Schlitter J., and Engelborghs Y. Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum. Proteins 28 (1997) 434-451
-
(1997)
Proteins
, vol.28
, pp. 434-451
-
-
Díaz, J.F.1
Wroblowski, B.2
Schlitter, J.3
Engelborghs, Y.4
-
30
-
-
0037197932
-
Conformational pathways in the gating of Escherichia coli mechanosensitive channel
-
Kong Y., Shen Y., Warth T.E., and Ma J. Conformational pathways in the gating of Escherichia coli mechanosensitive channel. Proc. Natl Acad. Sci. USA 99 (2002) 5999
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 5999
-
-
Kong, Y.1
Shen, Y.2
Warth, T.E.3
Ma, J.4
-
31
-
-
0035815288
-
Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
-
Young M.A., Gonfloni S., Superti-Furga G., Roux B., and Kuriyan J. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105 (2001) 115-126
-
(2001)
Cell
, vol.105
, pp. 115-126
-
-
Young, M.A.1
Gonfloni, S.2
Superti-Furga, G.3
Roux, B.4
Kuriyan, J.5
-
32
-
-
0003438040
-
-
Hoch J.A., and Silhavy T.J. (Eds), American Society for Microbiology Press, Washington, DC
-
In: Hoch J.A., and Silhavy T.J. (Eds). Two-Component Signal Transduction (1995), American Society for Microbiology Press, Washington, DC
-
(1995)
Two-Component Signal Transduction
-
-
-
33
-
-
0033599026
-
Structure of a transiently phosphorylated switch in bacterial signal transduction
-
Kern D., Volkman B.F., Luginbuhl P., Nohaile M.J., Kustu S., and Wemmer D.E. Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature 402 (1999) 894-898
-
(1999)
Nature
, vol.402
, pp. 894-898
-
-
Kern, D.1
Volkman, B.F.2
Luginbuhl, P.3
Nohaile, M.J.4
Kustu, S.5
Wemmer, D.E.6
-
34
-
-
0028927334
-
Three- dimensional solution structure of the N-terminal receiver domain of NtrC
-
Volkman B.F., Nohaile M.J., Amy N.K., Kustu S., and Wemmer D.E. Three- dimensional solution structure of the N-terminal receiver domain of NtrC. Biochemistry 34 (1995) 1413-1424
-
(1995)
Biochemistry
, vol.34
, pp. 1413-1424
-
-
Volkman, B.F.1
Nohaile, M.J.2
Amy, N.K.3
Kustu, S.4
Wemmer, D.E.5
-
35
-
-
0035937443
-
Two-state allosteric behavior in a single-domain signaling protein
-
Volkman B.F., Lipson D., Wemmer D.E., and Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science 291 (2001) 2429-2433
-
(2001)
Science
, vol.291
, pp. 2429-2433
-
-
Volkman, B.F.1
Lipson, D.2
Wemmer, D.E.3
Kern, D.4
-
36
-
-
0042165841
-
High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain
-
Hastings C.A., Lee S.Y., Cho H.S., Yan D., Kustu S., and Wemmer D.E. High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain. Biochemistry 42 (2003) 9081-9090
-
(2003)
Biochemistry
, vol.42
, pp. 9081-9090
-
-
Hastings, C.A.1
Lee, S.Y.2
Cho, H.S.3
Yan, D.4
Kustu, S.5
Wemmer, D.E.6
-
37
-
-
34250858152
-
Functional dynamics of response regulators using NMR relaxation techniques
-
Gardino A., and Kern D. Functional dynamics of response regulators using NMR relaxation techniques. Methods Enzymol. 423 (2007) 149-165
-
(2007)
Methods Enzymol.
, vol.423
, pp. 149-165
-
-
Gardino, A.1
Kern, D.2
-
38
-
-
33645317601
-
Molecular dynamic simulations of the N-terminal receiver domain of NtrC reveal intrinsic conformational flexibility in the inactive state
-
Hu X., and Wang Y. Molecular dynamic simulations of the N-terminal receiver domain of NtrC reveal intrinsic conformational flexibility in the inactive state. J. Biomol. Struct. Dyn. 23 (2006) 509-518
-
(2006)
J. Biomol. Struct. Dyn.
, vol.23
, pp. 509-518
-
-
Hu, X.1
Wang, Y.2
-
39
-
-
39649088661
-
Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles
-
Lätzer J., Shen T., and Wolynes P.G. Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles. Biochemistry 47 (2008) 2110-2122
-
(2008)
Biochemistry
, vol.47
, pp. 2110-2122
-
-
Lätzer, J.1
Shen, T.2
Wolynes, P.G.3
-
40
-
-
40549128343
-
Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling
-
Khalili M., and Wales D.J. Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling. J. Phys. Chem. B 112 (2008) 2456-2465
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 2456-2465
-
-
Khalili, M.1
Wales, D.J.2
-
41
-
-
0037441524
-
Refinement of protein structures in explicit solvent
-
Linge J.P., Williams M.A., Spronk C.A.E.M., Bonvin A.M.J.J., and Nilges M. Refinement of protein structures in explicit solvent. Proteins Struct. Funct. Genet. 50 (2003) 496-506
-
(2003)
Proteins Struct. Funct. Genet.
, vol.50
, pp. 496-506
-
-
Linge, J.P.1
Williams, M.A.2
Spronk, C.A.E.M.3
Bonvin, A.M.J.J.4
Nilges, M.5
-
43
-
-
0036234027
-
Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
-
Xia B., Tsui V., Case D.A., Dyson H.J., and Wright P.E. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J. Biomol. NMR 22 (2002) 317-331
-
(2002)
J. Biomol. NMR
, vol.22
, pp. 317-331
-
-
Xia, B.1
Tsui, V.2
Case, D.A.3
Dyson, H.J.4
Wright, P.E.5
-
44
-
-
2442610955
-
DRESS: a database of refined solution NMR structures
-
Nabuurs S.B., Nederveen A.J., Vranken W., Doreleijers J.F., Bonvin A.M.J.J., Vuister G.W., et al. DRESS: a database of refined solution NMR structures. Proteins Struct. Funct. Bioinf. 55 (2004) 483-486
-
(2004)
Proteins Struct. Funct. Bioinf.
, vol.55
, pp. 483-486
-
-
Nabuurs, S.B.1
Nederveen, A.J.2
Vranken, W.3
Doreleijers, J.F.4
Bonvin, A.M.J.J.5
Vuister, G.W.6
-
45
-
-
21044449889
-
RECOORD: a recalculated coordinate database of 500 proteins from the PDB using restraints from the BioMagResBank
-
Nederveen A.J., Doreleijers J.F., Vranken W., Miller Z., Spronk C.A.E.M., Nabuurs S.B., et al. RECOORD: a recalculated coordinate database of 500 proteins from the PDB using restraints from the BioMagResBank. Proteins Struct. Funct. Bioinf. 59 (2005) 662-672
-
(2005)
Proteins Struct. Funct. Bioinf.
, vol.59
, 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
-
46
-
-
23044509110
-
NMR data collection and analysis protocol for high-throughput protein structure determination
-
Liu G., Shen Y., Atreya H.S., Parish D., Shao Y., Sukumaran D.K., et al. NMR data collection and analysis protocol for high-throughput protein structure determination. Proc. Natl Acad. Sci. USA 102 (2005) 10487-10492
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 10487-10492
-
-
Liu, G.1
Shen, Y.2
Atreya, H.S.3
Parish, D.4
Shao, Y.5
Sukumaran, D.K.6
-
48
-
-
0025398721
-
WHAT IF: a molecular modeling and drug design program
-
Vriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graphics 8 (1990) 52-56
-
(1990)
J. Mol. Graphics
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
49
-
-
34547179849
-
Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology
-
Shen Y., and Bax A. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J. Biolmol. NMR 38 (2007) 289-302
-
(2007)
J. Biolmol. NMR
, vol.38
, pp. 289-302
-
-
Shen, Y.1
Bax, A.2
-
50
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
51
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell Jr. A.D., Bashford D., Bellott M., Dunbrack Jr. R.L., Evanseck J.D., Field M.J., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102 (1998) 3586-3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
-
52
-
-
0037671391
-
Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein
-
Pang A., Arinaminpathy Y., Sansom M.S.P., and Biggin P.C. Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein. FEBS Lett. 550 (2003) 168-174
-
(2003)
FEBS Lett.
, vol.550
, pp. 168-174
-
-
Pang, A.1
Arinaminpathy, Y.2
Sansom, M.S.P.3
Biggin, P.C.4
-
53
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
Henzler-Wildman K.A., Thai V., Lei M., Ott M., Wolf-Watz M., Fenn T., et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 450 (2007) 838-844
-
(2007)
Nature
, vol.450
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
Thai, V.2
Lei, M.3
Ott, M.4
Wolf-Watz, M.5
Fenn, T.6
-
54
-
-
0029075795
-
The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water
-
van Aalten D.M., Amadei A., Linssen A.B., Eijsink V.G., Vriend G., and Berendsen H.J. The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water. Proteins Struct. Funct. Genet. 22 (1995) 45-54
-
(1995)
Proteins Struct. Funct. Genet.
, vol.22
, pp. 45-54
-
-
van Aalten, D.M.1
Amadei, A.2
Linssen, A.B.3
Eijsink, V.G.4
Vriend, G.5
Berendsen, H.J.6
-
55
-
-
18144418170
-
Protein structural change upon ligand binding: linear response theory
-
Ikeguchi M., Ueno J., Sato M., and Kidera A. Protein structural change upon ligand binding: linear response theory. Phys. Rev. Lett. 94 (2005) 078102
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 078102
-
-
Ikeguchi, M.1
Ueno, J.2
Sato, M.3
Kidera, A.4
-
56
-
-
34547666968
-
How well can we understand large-scale protein motions using normal modes of elastic network models?
-
Yang L., Song G., and Jernigan R.L. How well can we understand large-scale protein motions using normal modes of elastic network models?. Biophys. J. 93 (2007) 920-929
-
(2007)
Biophys. J.
, vol.93
, pp. 920-929
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
57
-
-
36849039429
-
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
-
Henzler-Wildman K.A., Lei M., Thai V., Kerns S.J., Karplus M., and Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450 (2007) 913-916
-
(2007)
Nature
, vol.450
, pp. 913-916
-
-
Henzler-Wildman, K.A.1
Lei, M.2
Thai, V.3
Kerns, S.J.4
Karplus, M.5
Kern, D.6
-
58
-
-
33846847773
-
Conformational transitions of adenylate kinase: switching by cracking
-
Whitford P.C., Miyashita O., Levy Y., and Onuchic J.N. Conformational transitions of adenylate kinase: switching by cracking. J. Mol. Biol. 366 (2007) 1661-1671
-
(2007)
J. Mol. Biol.
, vol.366
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
59
-
-
17544365232
-
Finite temperature string method for the study of rare events
-
E W., Ren W., and Vanden-Eijnden E. Finite temperature string method for the study of rare events. J. Phys. Chem. B. 109 (2005) 6688
-
(2005)
J. Phys. Chem. B.
, vol.109
, pp. 6688
-
-
Weinan, E.1
Ren, W.2
Vanden-Eijnden, E.3
-
60
-
-
45949108535
-
Finding transition pathways using the string method with swarms of trajectories
-
Pan A.C., Sezer D., and Roux B. Finding transition pathways using the string method with swarms of trajectories. J. Phys. Chem. B. 112 (2008) 3432
-
(2008)
J. Phys. Chem. B.
, vol.112
, pp. 3432
-
-
Pan, A.C.1
Sezer, D.2
Roux, B.3
-
62
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program Dyana
-
Güntert P., Mumenthaler C., and Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program Dyana. J. Mol. Biol. 273 (1997) 283-298
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 283-298
-
-
Güntert, P.1
Mumenthaler, C.2
Wüthrich, K.3
-
63
-
-
84986512474
-
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. 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.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
64
-
-
10844247921
-
A modified TIP3P water potential for simulation with Ewald summation
-
Price D.J., and Brooks III C.L. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121 (2004) 10096
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 10096
-
-
Price, D.J.1
Brooks III, C.L.2
-
65
-
-
69449096502
-
-
Grubmüller, H. The Solvate Program Version 1.0. Web site
-
Grubmüller, H. The Solvate Program Version 1.0. Web site: http://www.mpibpc.mpg.de/groups/grubmueller/.
-
-
-
-
66
-
-
36749119973
-
Deformable stochastic boundaries in molecular dynamics
-
Brooks III C.L., and Karplus M. Deformable stochastic boundaries in molecular dynamics. J. Chem. Phys. 79 (1983) 6312
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 6312
-
-
Brooks III, C.L.1
Karplus, M.2
-
67
-
-
48749137581
-
Stochastic boundary conditions for molecular dynamics simulations of ST2 water
-
Brünger A., Brooks III C.L., and Karplus M. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 105 (1984) 495-500
-
(1984)
Chem. Phys. Lett.
, vol.105
, pp. 495-500
-
-
Brünger, A.1
Brooks III, C.L.2
Karplus, M.3
-
68
-
-
0038792211
-
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
-
Lee M.S., Feig M., Salsbury F.R., and Brooks III C.L. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J. Comput. Chem. 24 (2003) 1348-1356
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1348-1356
-
-
Lee, M.S.1
Feig, M.2
Salsbury, F.R.3
Brooks III, C.L.4
-
69
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell A.D., Feig M., and Brooks III C.L. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25 (2004) 1400-1415
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
Mackerell, A.D.1
Feig, M.2
Brooks III, C.L.3
-
70
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
-
Ryckaert J.P., Ciccotti G., and Berendsen H.J. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23 (1977) 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.3
-
71
-
-
0030700726
-
Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis
-
Ma J., and Karplus M. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J. Mol. Biol. 274 (1997) 114-131
-
(1997)
J. Mol. Biol.
, vol.274
, pp. 114-131
-
-
Ma, J.1
Karplus, M.2
-
74
-
-
69449102205
-
-
Sutanthavibul, S., Smith, B. V. & King, P. XFIG Drawing Program for the X Window System. Web site: http://www.xfig.org.
-
Sutanthavibul, S., Smith, B. V. & King, P. XFIG Drawing Program for the X Window System. Web site: http://www.xfig.org.
-
-
-
|