-
3
-
-
0022111715
-
Normal mode for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
-
Brooks B., Karplus M. Normal mode for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl Acad. Sci. USA. 82:1985;4995-4999.
-
(1985)
Proc. Natl Acad. Sci. USA
, vol.82
, pp. 4995-4999
-
-
Brooks, B.1
Karplus, M.2
-
4
-
-
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., 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
-
5
-
-
0001031179
-
Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
-
Brooks C. L., Karplus M., Pettitt B. M. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. Advan. Chem. Phys. 71:1988;1-249.
-
(1988)
Advan. Chem. Phys.
, vol.71
, pp. 1-249
-
-
Brooks, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
6
-
-
0000885331
-
Harmonic analysis of large systems. I. Methodology
-
Brooks B. R., Janežič D., Karplus M. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 16:1995;1522-1542.
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1522-1542
-
-
Brooks, B.R.1
Janežič, D.2
Karplus, M.3
-
7
-
-
0008994613
-
Extracting the energy barrier distribution of a disordered system from the instantaneous normal mode density of states: Applications to peptides and proteins
-
Choi J. K., Straub J. E. Extracting the energy barrier distribution of a disordered system from the instantaneous normal mode density of states: applications to peptides and proteins. J. Phys. Chem. 98:1994;10978-10987.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 10978-10987
-
-
Choi, J.K.1
Straub, J.E.2
-
8
-
-
33845281730
-
Simple intramolecular model potentials for water
-
Dang L. X., Pettitt B. M. Simple intramolecular model potentials for water. J. Phys. Chem. 91:1987;3349-3354.
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 3349-3354
-
-
Dang, L.X.1
Pettitt, B.M.2
-
10
-
-
0029156702
-
Molecular dynamics simulation of the solution structures of Ha- ras -p21 gdp and gtp complexes: Flexibility, possible hinges, and levers of the conformational transition
-
Díaz J. F., Wroblowski B., Engleborhs Y. Molecular dynamics simulation of the solution structures of Ha- ras -p21 gdp and gtp complexes: flexibility, possible hinges, and levers of the conformational transition. Biochemistry. 34:1995;12038-12047.
-
(1995)
Biochemistry
, vol.34
, pp. 12038-12047
-
-
Díaz, J.F.1
Wroblowski, B.2
Engleborhs, Y.3
-
11
-
-
0028216328
-
Guanine-nucleotide exchange factors: A family of positive regulators of Ras and related GTPases
-
Feig L. A. Guanine-nucleotide exchange factors: a family of positive regulators of Ras and related GTPases. Curr. Opin. Cell Biol. 6:1994;204-211.
-
(1994)
Curr. Opin. Cell Biol.
, vol.6
, pp. 204-211
-
-
Feig, L.A.1
-
12
-
-
0026778175
-
Simulation of the solution structure of the H-ras p21-GTP complex
-
Foley C. K., Pedersen L. G., Charifson P. S., Darden T. A., Wittinghofer A., Pai E. F., Anderson M. W. Simulation of the solution structure of the H-ras p21-GTP complex. Biochemistry. 31:1992;4951-4959.
-
(1992)
Biochemistry
, vol.31
, pp. 4951-4959
-
-
Foley, C.K.1
Pedersen, L.G.2
Charifson, P.S.3
Darden, T.A.4
Wittinghofer, A.5
Pai, E.F.6
Anderson, M.W.7
-
13
-
-
0027171116
-
H-ras
-
H-ras. Biochemistry. 32:1993;8411-8420.
-
(1993)
Biochemistry
, vol.32
, pp. 8411-8420
-
-
Franken, S.M.1
Scheidig, A.J.2
Krengel, U.3
Renslan, H.4
Lautwein, A.5
Geyer, M.6
Scheffzek, K.7
Good, R.S.8
Kalbitzer, H.R.9
Pai, E.F.10
Wittinghofer, A.11
-
14
-
-
0028174685
-
The hydration of ras p21 in solution during GTP hydrolysis based on solution X-ray scattering profile
-
Fujisawa T., Uraga T., Yamaizumi Z., Inoko Y., Nishimura S., Ueki T. The hydration of ras p21 in solution during GTP hydrolysis based on solution X-ray scattering profile. J. Biochem. 115:1994;875-880.
-
(1994)
J. Biochem.
, vol.115
, pp. 875-880
-
-
Fujisawa, T.1
Uraga, T.2
Yamaizumi, Z.3
Inoko, Y.4
Nishimura, S.5
Ueki, T.6
-
15
-
-
0000811664
-
Intrinsic GTPase activity distinguishes normal and oncogenic ras p21 molecules
-
Gibbs J. B., Sigal I. S., Poe M., Scolnick E. M. Intrinsic GTPase activity distinguishes normal and oncogenic ras p21 molecules. Proc. Natl Acad. Sci. USA. 81:1984;5704-5708.
-
(1984)
Proc. Natl Acad. Sci. USA
, vol.81
, pp. 5704-5708
-
-
Gibbs, J.B.1
Sigal, I.S.2
Poe, M.3
Scolnick, E.M.4
-
16
-
-
0021701376
-
Variational calculation of the normal modes of a large macromolecule: Methods and some initial results
-
Harrison R. W. Variational calculation of the normal modes of a large macromolecule: methods and some initial results. Biopolymers. 23:1984;2943-2949.
-
(1984)
Biopolymers
, vol.23
, pp. 2943-2949
-
-
Harrison, R.W.1
-
17
-
-
0000081668
-
Collective variable description of native protein dynamics
-
Hayward S., Go N. Collective variable description of native protein dynamics. Annu. Rev. Phys. Chem. 46:1995;223-250.
-
(1995)
Annu. Rev. Phys. Chem.
, vol.46
, pp. 223-250
-
-
Hayward, S.1
Go, N.2
-
18
-
-
0027208625
-
Identification of amino acids in p21ras involved in exchange factor interaction
-
Howe L. R., Marshell C. J. Identification of amino acids in p21ras involved in exchange factor interaction. Oncogenes. 8:1993;2583-2590.
-
(1993)
Oncogenes
, vol.8
, pp. 2583-2590
-
-
Howe, L.R.1
Marshell, C.J.2
-
19
-
-
0025015392
-
Anatomy of a conformational change: Hinged "lid" motion of the trioseposphate isomerase loop
-
Joseph D., Petsko G. A., Karplus M. Anatomy of a conformational change: hinged "lid" motion of the trioseposphate isomerase loop. Science. 249:1990;1425-1428.
-
(1990)
Science
, vol.249
, pp. 1425-1428
-
-
Joseph, D.1
Petsko, G.A.2
Karplus, M.3
-
20
-
-
0029958571
-
The GTP binding motif: Variations on a theme
-
Kjeldgaard M., Nyborg J., Clark B. F. The GTP binding motif: variations on a theme. FASEB J. 10:1996;1347-1368.
-
(1996)
FASEB J.
, vol.10
, pp. 1347-1368
-
-
Kjeldgaard, M.1
Nyborg, J.2
Clark, B.F.3
-
21
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
-
(1991)
J. Appl. Crystallog.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
22
-
-
0025904209
-
Rigid protein motion as a model for crystallographic temperature factors
-
Kuriyan J., Weis W. Rigid protein motion as a model for crystallographic temperature factors. Proc Natl Acad. Sci. USA. 88:1991;2773-2777.
-
(1991)
Proc Natl Acad. Sci. USA
, vol.88
, pp. 2773-2777
-
-
Kuriyan, J.1
Weis, W.2
-
24
-
-
4243223070
-
NAS, in press
-
Ma, Karplus A. NAS, in press. 00. 00:1997;00-00.
-
(1997)
00
, vol.0
, pp. 00-00
-
-
Ma1
Karplus, A.2
-
25
-
-
23544437400
-
J. Phy. Chem., in press
-
Mackerell. J. Phy. Chem., in press. 00. 0000:1997;00-00.
-
(1997)
00
, vol.0
, pp. 00-00
-
-
MacKerell1
-
26
-
-
0011186077
-
Ha- ras proteins exhibit GTPase activity: Point mutations that activate ha- ras gene products result in decreased GTPase activity
-
Manne V., Bekesi E., Kung H. Ha- ras proteins exhibit GTPase activity: point mutations that activate ha- ras gene products result in decreased GTPase activity. Proc. Natl Acad. Sci. USA. 82:1985;376-380.
-
(1985)
Proc. Natl Acad. Sci. USA
, vol.82
, pp. 376-380
-
-
Manne, V.1
Bekesi, E.2
Kung, H.3
-
27
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
Marques O., Sanejouand Y. H. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins: Struct. Funct. Genet. 23:1995;557-560.
-
(1995)
Proteins: Struct. Funct. Genet.
, vol.23
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.H.2
-
29
-
-
0024502703
-
Ras GTPase activating protein: Signal transmitter and signal terminator
-
McCormick F. ras GTPase activating protein: signal transmitter and signal terminator. Cell. 56:1989;5-8.
-
(1989)
Cell
, vol.56
, pp. 5-8
-
-
McCormick, F.1
-
31
-
-
0025117674
-
Molecular switch for signal transduction: Structural differences between active and inactive forms of protooncogenicras p21
-
Milburn M. V., Tong L., deVos A. M., Brünger A., Yamaizumi Z., Nishimura S., Kim S. H. Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenicras p21. Science. 247:1990;939-945.
-
(1990)
Science
, vol.247
, pp. 939-945
-
-
Milburn, M.V.1
Tong, L.2
Devos, A.M.3
Brünger, A.4
Yamaizumi, Z.5
Nishimura, S.6
Kim, S.H.7
-
32
-
-
0025195630
-
NRASprotooncogene product, is accompanied by a conformational change in the wild-type protein: Use of a single fluorescent probe at the catalytic site
-
NRASprotooncogene product, is accompanied by a conformational change in the wild-type protein: use of a single fluorescent probe at the catalytic site. Proc. Natl Acad. Sci. USA. 87:1990;3562-3565.
-
(1990)
Proc. Natl Acad. Sci. USA
, vol.87
, pp. 3562-3565
-
-
Neal, S.E.1
Eccleston, J.F.2
Webb, M.R.3
-
33
-
-
0025310575
-
Refined crystal structure of the triphosphate conformation of H- ras p21 at 1.35 å resolution: Implications for the mechanism of GTP hydrolysis
-
Pai E. F., Krengel U., Petsko G. A., Goody R. S., Kabsch W., Wittinghofer A. Refined crystal structure of the triphosphate conformation of H- ras p21 at 1.35 å resolution: implications for the mechanism of GTP hydrolysis. EMBO J. 9:1990;2351-2359.
-
(1990)
EMBO J.
, vol.9
, pp. 2351-2359
-
-
Pai, E.F.1
Krengel, U.2
Petsko, G.A.3
Goody, R.S.4
Kabsch, W.5
Wittinghofer, A.6
-
34
-
-
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
-
Sanejouand Y. H. 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. 9:1996;671-677.
-
(1996)
Protein Eng.
, vol.9
, pp. 671-677
-
-
Sanejouand, Y.H.1
-
35
-
-
0027917990
-
The crystal structure of elongation factor EF-Tu from thermus acquaticus in the GTP conformation
-
Scheffzek K., Lautwein A., Kabsch W., Ahmadian M. R., Wittinghofer A. The crystal structure of elongation factor EF-Tu from thermus acquaticus in the GTP conformation. Structure. 1:1993;35-50.
-
(1993)
Structure
, vol.1
, pp. 35-50
-
-
Scheffzek, K.1
Lautwein, A.2
Kabsch, W.3
Ahmadian, M.R.4
Wittinghofer, A.5
-
36
-
-
0029829561
-
Crystal structure of the GTPase-activating domain of human p120GAP and implications for the interaction with Ras
-
Scheffzek K., Lautwein A., Kabsch W., Ahmadian M. R., Wittinghofer A. Crystal structure of the GTPase-activating domain of human p120GAP and implications for the interaction with Ras. Nature. 384:1996;591-596.
-
(1996)
Nature
, vol.384
, pp. 591-596
-
-
Scheffzek, K.1
Lautwein, A.2
Kabsch, W.3
Ahmadian, M.R.4
Wittinghofer, A.5
-
37
-
-
0021126650
-
Biological properties of human c-Has- ras 1 genes mutated at codon 12
-
Seeburg P. H., Colby W. W., Capon D. J., Goeddel D. V., Levinson A. D. Biological properties of human c-Has- ras 1 genes mutated at codon 12. Nature. 312:1984;71-75.
-
(1984)
Nature
, vol.312
, pp. 71-75
-
-
Seeburg, P.H.1
Colby, W.W.2
Capon, D.J.3
Goeddel, D.V.4
Levinson, A.D.5
-
38
-
-
0027431378
-
Protein hydration elucidated by molecular dynamics simulation
-
Steinbach P. J., Brooks B. Protein hydration elucidated by molecular dynamics simulation. Proc. Natl Acad. Sci. USA. 90:1993;9135-9139.
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 9135-9139
-
-
Steinbach, P.J.1
Brooks, B.2
-
39
-
-
0001239392
-
The instantaneous normal modes of liquids
-
Stratt R. M. The instantaneous normal modes of liquids. Acc. Chem. Res. 28:1995;201-207.
-
(1995)
Acc. Chem. Res.
, vol.28
, pp. 201-207
-
-
Stratt, R.M.1
-
40
-
-
0000118827
-
Harmonic and quasiharmonic description of crambin
-
Teeter M. M., Case D. A. Harmonic and quasiharmonic description of crambin. J. Phys. Chem. 94:1990;8091-8097.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8091-8097
-
-
Teeter, M.M.1
Case, D.A.2
-
41
-
-
0030004936
-
Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase
-
Thomas A., Field M. J., Mouawad L., Perahia D. Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase. J. Mol. Biol. 257:1996a;1070-1087.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 1070-1087
-
-
Thomas, A.1
Field, M.J.2
Mouawad, L.3
Perahia, D.4
-
42
-
-
0030599027
-
Analysis of the low frequency normal modes of the R state of aspartate transcarbamylaseand a comparison with the T state modes
-
Thomas A., Field M. J., Perahia D. Analysis of the low frequency normal modes of the R state of aspartate transcarbamylaseand a comparison with the T state modes. J. Mol. Biol. 261:1996b;490-506.
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 490-506
-
-
Thomas, A.1
Field, M.J.2
Perahia, D.3
-
43
-
-
0028360307
-
The contribution of vibrational entropy to molecular association
-
Tidor B., Karplus M. The contribution of vibrational entropy to molecular association. J. Mol. Biol. 238:1994;405-414.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 405-414
-
-
Tidor, B.1
Karplus, M.2
-
44
-
-
0026086679
-
Crystal structures at 2.2 Å resolution of the catalytic domains of normal ras protein and an oncogenic mutant complexed with GDP
-
Tong L., de Vos A. M., Milburn M. V., Kim S.-H. Crystal structures at 2.2 Å resolution of the catalytic domains of normal ras protein and an oncogenic mutant complexed with GDP. J. Mol. Biol. 217:1991;503-516.
-
(1991)
J. Mol. Biol.
, vol.217
, pp. 503-516
-
-
Tong, L.1
De Vos, A.M.2
Milburn, M.V.3
Kim, S.-H.4
-
45
-
-
0025740753
-
The structure of ras protein: A model for a universal molecular switch
-
Wittinghofer A., Pai E. The structure of ras protein: a model for a universal molecular switch. Trends Biochem. Sci. 10:1991;382-387.
-
(1991)
Trends Biochem. Sci.
, vol.10
, pp. 382-387
-
-
Wittinghofer, A.1
Pai, E.2
|