-
1
-
-
0034127361
-
Collective protein dynamics in relation to function
-
Berendsen,H.J.C. and Hayward,S. (2000) Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol., 10, 165-169.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 165-169
-
-
Berendsen, H.J.C.1
Hayward, S.2
-
2
-
-
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
-
3
-
-
0000991642
-
Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
-
Brooks,B.R. and Karplus,M. (1983) Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl Acad. Sci., USA, 80, 6571-6575.
-
(1983)
Proc. Natl. Acad. Sci., USA
, vol.80
, pp. 6571-6575
-
-
Brooks, B.R.1
Karplus, M.2
-
4
-
-
0003525155
-
-
John Wiley & Sons, New York
-
Brooks III,C.L., Karplus,M. and Pettitt,B.M. (1988) Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics, John Wiley & Sons, New York.
-
(1988)
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
-
-
Brooks III, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
6
-
-
0037436340
-
Mega-Dalton biomolecular motion captured from electron microscopy reconstructions
-
Chacon,P., Tama,F. and Wriggers,W. (2003) Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol., 326, 485-492.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 485-492
-
-
Chacon, P.1
Tama, F.2
Wriggers, W.3
-
7
-
-
0027535421
-
Crevice-forming mutants in the rigid core of bovine pancreatic trypsin inhibitor: Crystal structures of F22A, Y23A, N43G, and F45A
-
Danishefsky,A.T., Housset,D., Kim,K.S., Tao,F., Fuchs,J., Woodward,C., and Wlodawer,A. (1993) Crevice-forming mutants in the rigid core of bovine pancreatic trypsin inhibitor: crystal structures of F22A, Y23A, N43G, and F45A. Protein Sci., 2, 577-587.
-
(1993)
Protein Sci.
, vol.2
, pp. 577-587
-
-
Danishefsky, A.T.1
Housset, D.2
Kim, K.S.3
Tao, F.4
Fuchs, J.5
Woodward, C.6
Wlodawer, A.7
-
8
-
-
0037246863
-
MolNovDB: Analysis and visualization of conformational change and structural flexibility
-
Echols,N., Milburn,D. and Gerstein,M. (2003) MolNovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acid Res., 31, 478-482.
-
(2003)
Nucleic Acid Res.
, vol.31
, pp. 478-482
-
-
Echols, N.1
Milburn, D.2
Gerstein, M.3
-
9
-
-
0025292406
-
Structural effects induced by removal of a disulfide-bridge: The X-ray structure of the C30A/C51A mutant of basic pancreatic trypsin inhibitor at 1.6 Å
-
Eigenbrot,C., Randal,M., and Kossiakoff,A.A. (1990) Structural effects induced by removal of a disulfide-bridge: the X-ray structure of the C30A/C51A mutant of basic pancreatic trypsin inhibitor at 1.6 Å. Protein Eng., 3, 591-598.
-
(1990)
Protein Eng.
, vol.3
, pp. 591-598
-
-
Eigenbrot, C.1
Randal, M.2
Kossiakoff, A.A.3
-
10
-
-
0025066772
-
Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion
-
Gibrat,J.F. and Go,N. (1990) Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins, 8, 258-279.
-
(1990)
Proteins
, vol.8
, pp. 258-279
-
-
Gibrat, J.F.1
Go, N.2
-
11
-
-
0020771265
-
Dynamics of a small globular protein in terms of low-frequency vibrational modes
-
Go,N., Noguti,T. and Nishikawa,T. (1983) Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl Acad. Sci., USA, 80, 3696-3700.
-
(1983)
Proc. Natl. Acad. Sci., USA
, vol.80
, pp. 3696-3700
-
-
Go, N.1
Noguti, T.2
Nishikawa, T.3
-
12
-
-
0000081668
-
Collective variable description of native protein dynamics
-
Hayward,S. and Go,N. (1995) Collective variable description of native protein dynamics. Annu. Rev. Phys. Chem., 46, 223-250.
-
(1995)
Annu. Rev. Phys. Chem.
, vol.46
, pp. 223-250
-
-
Hayward, S.1
Go, N.2
-
13
-
-
0030888546
-
Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
-
Hayward,S., Kitao,A. and Berendsen,H.J. (1997) Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins, 27, 425-437.
-
(1997)
Proteins
, vol.27
, pp. 425-437
-
-
Hayward, S.1
Kitao, A.2
Berendsen, H.J.3
-
14
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen,K. (1998) Analysis of domain motions by approximate normal mode calculations. Proteins, 33, 417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
15
-
-
0001962564
-
The molecular modeling toolkit: A new approach to molecular simulations
-
Hinsen,K. (2000) The molecular modeling toolkit: A new approach to molecular simulations. J. Comp. Chem., 21, 79-85.
-
(2000)
J. Comp. Chem.
, vol.21
, pp. 79-85
-
-
Hinsen, K.1
-
16
-
-
0025753631
-
Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme
-
Horiuchi,T. and Go,N. (1991) Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme. Proteins, 10, 106-116.
-
(1991)
Proteins
, vol.10
, pp. 106-116
-
-
Horiuchi, T.1
Go, N.2
-
17
-
-
0025899958
-
Crystal structure of a Y35G mutant of bovine pancreatic trypsin inhibitor
-
Housset,D., Kim,K.S., Fuchs,J., Woodward,C. and Wlodawer,A. (1991) Crystal structure of a Y35G mutant of bovine pancreatic trypsin inhibitor. J. Mol. Biol., 220, 757-770.
-
(1991)
J. Mol. Biol.
, vol.220
, pp. 757-770
-
-
Housset, D.1
Kim, K.S.2
Fuchs, J.3
Woodward, C.4
Wlodawer, A.5
-
18
-
-
0026663419
-
Normal mode refinement: Crystallographic refinement of protein dynamics structure. I. Theory and test by simulated diffraction data
-
Kidera,A. and Go,N. (1992) Normal mode refinement: crystallographic refinement of protein dynamics structure. I. Theory and test by simulated diffraction data. J. Mol. Biol., 225, 457-475.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 457-475
-
-
Kidera, A.1
Go, N.2
-
19
-
-
0033856299
-
Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis
-
Kikuchi,H., Wako,H., Yura,K., Go,M. and Mimuro,M. (2000) Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis. Biophys. J., 79, 1587-1600.
-
(2000)
Biophys. J.
, vol.79
, pp. 1587-1600
-
-
Kikuchi, H.1
Wako, H.2
Yura, K.3
Go, M.4
Mimuro, M.5
-
20
-
-
0033117937
-
Investigating protein dynamics in collective coordinate space
-
Kitao,A. and Go,N. (1999) Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol., 9, 164-169.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 164-169
-
-
Kitao, A.1
Go, N.2
-
21
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
Krebs,W.G., Alexandrov,V., Wilson,C.A., Echols,N. Yu,H. and Gerstein,M. (2002) Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic. Proteins, 48, 682-695.
-
(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
-
22
-
-
0022419152
-
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
-
Levitt,M., Sander,C. and Stern,P.S. (1985) Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol., 181, 423-447.
-
(1985)
J. Mol. Biol.
, vol.181
, pp. 423-447
-
-
Levitt, M.1
Sander, C.2
Stern, P.S.3
-
23
-
-
0021449809
-
Quasi-harmonic method for studying very low frequency modes in proteins
-
Levy,R.M. Srinivasan,R. and Olson,W.K. (1984) Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers, 23, 1099-1112.
-
(1984)
Biopolymers
, vol.23
, pp. 1099-1112
-
-
Levy, R.M.1
Srinivasan, R.2
Olson, W.K.3
-
24
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
Marques,O. and Sanejouand,Y.H. (1995) Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins, 23, 557-560.
-
(1995)
Proteins
, vol.23
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.H.2
-
25
-
-
0033548074
-
Enzyme specificity under dynamic control: A normal mode analysis of alpha-lytic protease
-
Miller,D.W. and Agard,D.A. (1999) Enzyme specificity under dynamic control: a normal mode analysis of alpha-lytic protease. J. Mol. Biol., 286, 267-278.
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 267-278
-
-
Miller, D.W.1
Agard, D.A.2
-
26
-
-
0020813608
-
Dynamics of native globular proteins in terms of dihedral angles
-
Noguti,T. and Go,N. (1983a) Dynamics of native globular proteins in terms of dihedral angles. J. Phys. Soc. Jpn., 52, 3283-3288.
-
(1983)
J. Phys. Soc. Jpn.
, vol.52
, pp. 3283-3288
-
-
Noguti, T.1
Go, N.2
-
27
-
-
0020831001
-
A method of rapid calculation of a second derivative matrix of conformational energy for large molecules
-
Noguti,T. and Go,N. (1983b) A method of rapid calculation of a second derivative matrix of conformational energy for large molecules. J. Phys. Soc. Jpn., 52, 3685-3690.
-
(1983)
J. Phys. Soc. Jpn.
, vol.52
, pp. 3685-3690
-
-
Noguti, T.1
Go, N.2
-
28
-
-
0029119568
-
RASMOL: Biomolecular graphics for all
-
Sayle,R.A. (1995) RASMOL: biomolecular graphics for all. TIBS, 20, 374-376.
-
(1995)
TIBS
, vol.20
, pp. 374-376
-
-
Sayle, R.A.1
-
29
-
-
0030004936
-
Analysis of the low-frequency normal modes of the T-state of aspartate transcarbamylase
-
Thomas,A., Field,M.J., Mouawad,L. and Perahia,D. (1996a) Analysis of the low-frequency normal modes of the T-state of aspartate transcarbamylase. J. Mol. Biol., 257, 1070-1087.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 1070-1087
-
-
Thomas, A.1
Field, M.J.2
Mouawad, L.3
Perahia, D.4
-
30
-
-
0030599027
-
Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes
-
Thomas,A., Field,M.J. and Perahia,D. (1996b) Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes. J. Mol. Biol., 261, 490-506.
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 490-506
-
-
Thomas, A.1
Field, M.J.2
Perahia, D.3
-
31
-
-
0029633151
-
FEDER/2: Program for static and dynamic conformational energy analysis of macro-molecules in dihedral angle space
-
Wako,H., Endo,S., Nagayama,K. and Go,N. (1995) FEDER/2: program for static and dynamic conformational energy analysis of macro-molecules in dihedral angle space. Comp. Phys. Comm., 91, 233-251.
-
(1995)
Comp. Phys. Comm.
, vol.91
, pp. 233-251
-
-
Wako, H.1
Endo, S.2
Nagayama, K.3
Go, N.4
-
32
-
-
84988123096
-
Algorithm for rapid calculation of hessian of conformational energy function of protein by supercomputer
-
Wako,H. and Go,N. (1987) Algorithm for rapid calculation of hessian of conformational energy function of protein by supercomputer. J. Comp. Chem., 8, 625-635.
-
(1987)
J. Comp. Chem.
, vol.8
, pp. 625-635
-
-
Wako, H.1
Go, N.2
-
33
-
-
0029835942
-
A comparative study of dynamic structures between phage 434 Cro and repressor proteins by normal mode analysis
-
Wako,H., Tachikawa,M. and Ogawa,A. (1996) A comparative study of dynamic structures between phage 434 Cro and repressor proteins by normal mode analysis. Proteins, 26, 72-80.
-
(1996)
Proteins
, vol.26
, pp. 72-80
-
-
Wako, H.1
Tachikawa, M.2
Ogawa, A.3
-
34
-
-
0021603710
-
Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II
-
Wlodawer,A., Walter,J., Huber,R. and Sjolin,L. (1984) Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II. J. Mol. Biol., 180, 301-329.
-
(1984)
J. Mol. Biol.
, vol.180
, pp. 301-329
-
-
Wlodawer, A.1
Walter, J.2
Huber, R.3
Sjolin, L.4
|