-
1
-
-
0017163950
-
The hinge-bending mode in lysozyme
-
J.A. McCammon, B.R. Gelin, M. Karplus, and P.G. Wolynes. The hinge-bending mode in lysozyme. Nature,262: 325-326, 1976.
-
(1976)
Nature
, vol.262
, pp. 325-326
-
-
McCammon, J.A.1
Gelin, B.R.2
Karplus, M.3
Wolynes, P.G.4
-
2
-
-
0022111715
-
Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
-
B.R. Brooks and M. Karplus. Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme. Proc. Natl Acad. Sci. USA,82: 4995-4999, 1985.
-
(1985)
Proc. Natl Acad. Sci. USA
, vol.82
, pp. 4995-4999
-
-
Brooks, B.R.1
Karplus, M.2
-
3
-
-
0022419152
-
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
-
M. Levitt, C. Sander, and P.S. Stern. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol.,181: 423-447, 1985.
-
(1985)
J. Mol. Biol
, vol.181
, pp. 423-447
-
-
Levitt, M.1
Sander, C.2
Stern, P.S.3
-
4
-
-
0021701376
-
Variational calculation of the normal modes of large macromolecules: Methods and some initial results
-
W. Harrison. Variational calculation of the normal modes of large macromolecules: methods and some initial results. Biopolymers,23: 2943-2949, 1984.
-
(1984)
Biopolymers
, vol.23
, pp. 2943-2949
-
-
Harrison, W.1
-
5
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
O. Marques and Y.-H. Sanejouand. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins,23: 557-560, 1995.
-
(1995)
Proteins
, vol.23
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.-H.2
-
6
-
-
0029374782
-
Computation of low-frequency normal modes in macromolecules: Improvements to the method of diagonalization in a mixed basis and application to hemoglobin
-
D. Perahia and L. Mouawad. Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin. Comput. Chem.,19: 241-246, 1995.
-
(1995)
Comput. Chem
, vol.19
, pp. 241-246
-
-
Perahia, D.1
Mouawad, L.2
-
7
-
-
0029937635
-
Motions in hemoglobin studied by normal mode analysis and energy minimization: Evidence for the existence of tertiary t-like, quaternary r-like intermediate structures
-
L. Mouawad and D. Perahia. Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures. J. Mol. Biol.,258: 393-410, 1996.
-
(1996)
J. Mol. Biol
, vol.258
, pp. 393-410
-
-
Mouawad, L.1
Perahia, D.2
-
8
-
-
0033135638
-
Effective energy function for proteins in solution
-
T. Lazaridis and M. Karplus. Effective energy function for proteins in solution. Proteins,35:133-152,1999.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
9
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
M. Schaefer and M. Karplus. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem.,100:1578-1599, 1996.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
10
-
-
0035501755
-
Protein molecular dynamics with the generalized born/ace solvent model
-
N. Calimet, M. Schaefer, and T. Simonson. Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins,45:144-158, 2001.
-
(2001)
Proteins
, vol.45
, pp. 144-158
-
-
Calimet, N.1
Schaefer, M.2
Simonson, T.3
-
11
-
-
1142274273
-
Analysis of functional motions in brownian molecular machines with an efficient block normal mode approach: Myosin-ii and ca(2+)-atpase
-
G. Li and Q. Cui. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca(2+)-ATPase. Biophys.J,86: 743-763, 2004.
-
(2004)
Biophys.J
, vol.86
, pp. 743-763
-
-
Li, G.1
Cui, Q.2
-
12
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
F. Tama and Y.-H. Sanejouand. Conformational change of proteins arising from normal mode calculations. Protein Eng.,14:1-6, 2001.
-
(2001)
Protein Eng
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.-H.2
-
13
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
A.R. Atilgan, S.R. Durell, R.L. Jernigan, M.C. Demirel, O. Keskin, and I. Bahar. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys.J.,80: 505-515, 2001.
-
(2001)
Biophys.J
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
14
-
-
0036077875
-
Simplified normal modes analysis of conformational transitions in dna-dependant polymerases: The elastic network model
-
M. Delarue and Y.-H. Sanejouand. Simplified normal modes analysis of conformational transitions in DNA-dependant polymerases: the elastic network model. J. Mol. Biol.,320:1011-1024, 2002.
-
(2002)
J. Mol. Biol
, vol.320
, pp. 1011-1024
-
-
Delarue, M.1
Sanejouand, Y.-H.2
-
15
-
-
0000197372
-
Low-amplitude elastic motions in proteins from a single-parameter atomic analysis
-
M.M. Tirion. Low-amplitude elastic motions in proteins from a single-parameter atomic analysis. Phys. Rev. Lett.,77:1905-1908,1996.
-
(1996)
Phys. Rev. Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
16
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
I. Bahar, A.R. Atilgan, and B. Erman. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Design,2: 173-181, 1997.
-
(1997)
Fold. Design
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
17
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
K. Hinsen. Analysis of domain motions by approximate normal mode calculations. Proteins,33: 417-429, 1998.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
18
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
F. Tama, F.-X. Gadea, O. Marques, and Y.-H. Sanejouand. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins,41: 1-7, 2000.
-
(2000)
Proteins
, vol.41
, pp. 1-7
-
-
Tama, F.1
Gadea, F.-X.2
Marques, O.3
Sanejouand, Y.-H.4
-
19
-
-
0036382958
-
Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
-
F. Tama, W. Wriggers, and C.L. Brooks III. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol.,321: 297-305, 2002.
-
(2002)
J. Mol. Biol
, vol.321
, pp. 297-305
-
-
Tama, F.1
Wriggers, W.2
Brooks, C.L.3
-
20
-
-
2442567233
-
Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements
-
S. Hayward. Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. J. Mol. Biol.,339:1001-1021, 2004.
-
(2004)
J. Mol. Biol
, vol.339
, pp. 1001-1021
-
-
Hayward, S.1
-
21
-
-
0026244229
-
Molscript: A program to produce both detailed and schematic plots of protein structures
-
P. Kraulis. Molscript: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr.,24: 946-950,1991.
-
(1991)
J. Appl. Crystallogr
, vol.24
, pp. 946-950
-
-
Kraulis, P.1
-
22
-
-
84986512474
-
Charmm: A program for macromolecular energy, minimization, and dynamics calculations
-
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem.,4:187-217,1983.
-
(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
-
23
-
-
0000885331
-
Harmonic-analysis of large systems. 1. Methodology
-
B.R. Brooks, D. Janezic, and M. Karplus. Harmonic-analysis of large systems. 1. Methodology. J. Comput. Chem.,16:1522-1542, 1995.
-
(1995)
J. Comput. Chem
, vol.16
, pp. 1522-1542
-
-
Brooks, B.R.1
Janezic, D.2
Karplus, M.3
-
25
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
W.G. Krebs, V. Alexandrov, C.A. Wilson, N. Echols, H. Yu, and M. Gerstein. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins,48: 682-695, 2002.
-
(2002)
Proteins
, vol.48
, pp. 682-695
-
-
Krebs, W.G.1
Alexandrov, V.2
Wilson, C.A.3
Echols, N.4
Yu, H.5
Gerstein, M.6
-
26
-
-
0020488742
-
Collective variable description of small-amplitude conformational fluctuations in a globular protein
-
T. Noguti and N. Go. Collective variable description of small-amplitude conformational fluctuations in a globular protein. Nature,296: 776-778, 1982.
-
(1982)
Nature
, vol.296
, pp. 776-778
-
-
Noguti, T.1
Go, N.2
-
27
-
-
0025109873
-
Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction
-
Y. Seno and N. Go. Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction. J. Mol. Biol.,216: 95-109,1990.
-
(1990)
J. Mol. Biol
, vol.216
, pp. 95-109
-
-
Seno, Y.1
Go, N.2
-
28
-
-
0027576952
-
Dimb: Diagonalization in a mixed basis. A method to compute low-frequency normal modes for large macromolecules
-
L. Mouawad and D. Perahia. DIMB: Diagonalization in a mixed basis. A method to compute low-frequency normal modes for large macromolecules. Biopolymers, 33: 569-611, 1993.
-
(1993)
Biopolymers
, vol.33
, pp. 569-611
-
-
Mouawad, L.1
Perahia, D.2
-
29
-
-
0028454915
-
A new approach for determining low-frequency normal modes in macromolecules
-
P. Durand, G. Trinquier, and Y.H. Sanejouand. A new approach for determining low-frequency normal modes in macromolecules. Biopolymers,34: 759-771,1994.
-
(1994)
Biopolymers
, vol.34
, pp. 759-771
-
-
Durand, P.1
Trinquier, G.2
Sanejouand, Y.H.3
-
30
-
-
0036840202
-
A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to ca(2+)-atpase
-
G. Li and Q. Cui. A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca(2+)-ATPase. Biophys. J.,83: 2457-2474, 2002.
-
(2002)
Biophys. J
, vol.83
, pp. 2457-2474
-
-
Li, G.1
Cui, Q.2
-
31
-
-
0002133110
-
Mbo(N)d: A multibody method for long-time molecular dynamics simulations
-
H.M. Chun, C.E. Padilla, D.N. Chin, M. Watanabe, V.I. Karlov, H.E. Alper, K. Soosaar, K.B. Blair, O.M. Becker, L.S.D. Caves, R. Nagle, D.N. Haney, and B.L. Farmer. MBO(N)D: A multibody method for long-time molecular dynamics simulations. J. Comput. Chem.,21:159-184, 2000.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 159-184
-
-
Chun, H.M.1
Padilla, C.E.2
Chin, D.N.3
Watanabe, M.4
Karlov, V.I.5
Alper, H.E.6
Soosaar, K.7
Blair, K.B.8
Becker, O.M.9
Caves, L.S.D.10
Nagle, R.11
Haney, D.N.12
Farmer, B.L.13
-
32
-
-
37649030035
-
Exploring the natural conformational changes of the c-terminal domain of calmodulin
-
J. Elezgaray, G. Marcou, and Y.-H. Sanejouand. Exploring the natural conformational changes of the C-terminal domain of calmodulin. Phys. Rev. E,66: 31908-31915, 2002.
-
(2002)
Phys. Rev. E
, vol.66
, pp. 31908-31915
-
-
Elezgaray, J.1
Marcou, G.2
Sanejouand, Y.-H.3
-
33
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
F. Tama, M. Valle, J. Frank, and C.L. Brooks III. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl Acad. Sci. USA,100: 9319-9323, 2004.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks, C.L.4
-
34
-
-
3242883858
-
On the potential of normal mode analysis for solving difficult molecular replacement problems
-
K. Suhre and Y.-H. Sanejouand. On the potential of normal mode analysis for solving difficult molecular replacement problems. Act. Cryst. D,60: 796-799,2004.
-
(2004)
Act. Cryst. D
, vol.60
, pp. 796-799
-
-
Suhre, K.1
Sanejouand, Y.-H.2
-
35
-
-
3242875210
-
Elnémo: A normal mode server for protein movement analysis and the generation of templates for molecular replacement
-
K. Suhre and Y.-H. Sanejouand. Elnémo: A normal mode server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res.,32: W610-W614, 2004.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. W610-W614
-
-
Suhre, K.1
Sanejouand, Y.-H.2
-
36
-
-
0037079578
-
Dynamics of large proteins through hierarchical levels of coarse-grained structures
-
P. Doruker, R.L. Jernigan, and I. Bahar. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem.,23: 119-127, 2002.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 119-127
-
-
Doruker, P.1
Jernigan, R.L.2
Bahar, I.3
-
37
-
-
0030700726
-
Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis
-
J. Ma and M. Karplus. Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis. J. Mol. Biol.,274: 114-131, 1997.
-
(1997)
J. Mol. Biol
, vol.274
, pp. 114-131
-
-
Ma, J.1
Karplus, M.2
-
38
-
-
85015733852
-
-
Paul Sabatier University, Toulouse (France
-
F. Tama. Ph. D. Thesis. Paul Sabatier University, Toulouse (France), 2000.
-
(2000)
Ph. D. Thesis
-
-
Tama, F.1
-
39
-
-
0032530836
-
Adatabase of macromolecular motions
-
M. Gerstein and W.G. Krebs. Adatabase of macromolecular motions. Nucleic Acids Res.,26: 4280-4290,1998.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.G.2
-
40
-
-
0026065644
-
Crystal structure of unliganded escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding
-
C. Bystroff and J. Kraut. Crystal structure of unliganded Escherichia coli dihydrofolate reductase. ligand-induced conformational changes and cooperativity in binding. Biochemistry,30: 2227-2239, 1991.
-
(1991)
Biochemistry
, vol.30
, pp. 2227-2239
-
-
Bystroff, C.1
Kraut, J.2
-
41
-
-
0029791008
-
Normal-mode analysis suggests important flexibility between the two n-terminal domains of cd4 and supports the hypothesis of a conformational change in cd4 upon hiv binding
-
Y.-H. Sanejouand. Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding. Protein Eng.,9: 671-677,1996.
-
(1996)
Protein Eng
, vol.9
, pp. 671-677
-
-
Sanejouand, Y.-H.1
-
42
-
-
0043238084
-
Dynamical properties of the mscl of escherichia coli: A normal mode analysis
-
H. Valadie, J.-J. Lacapere, Y.-H. Sanejouand, and C. Etchebest. Dynamical properties of the Mscl of Escherichia coli: A normal mode analysis. J. Mol. Biol.,332: 657-674, 2003.
-
(2003)
J. Mol. Biol
, vol.332
, pp. 657-674
-
-
Valadie, H.1
Lacapere, J.-J.2
Sanejouand, Y.-H.3
Etchebest, C.4
-
43
-
-
1642355235
-
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
-
F. Tama, O. Miyashita, and C.L. Brooks III. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol.,337: 985-999, 2004.
-
(2004)
J. Mol. Biol
, vol.337
, pp. 985-999
-
-
Tama, F.1
Miyashita, O.2
Brooks, C.L.3
-
44
-
-
2342518038
-
On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
-
M. Delarue and P. Dumas. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc. Natl Acad. Sci. USA,101: 6957-6962,2004.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 6957-6962
-
-
Delarue, M.1
Dumas, P.2
|