-
2
-
-
0029985860
-
An efficient method for sampling the essential subspace of proteins
-
Amadei, A., A. B. M. Linssen, B. L. de Groot, D. M. F. van Aalten, and H. J. C. Berendsen. 1996. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn. 13:615-625.
-
(1996)
J. Biomol. Struct. Dyn.
, vol.13
, pp. 615-625
-
-
Amadei, A.1
Linssen, A.B.M.2
De Groot, B.L.3
Van Aalten, D.M.F.4
Berendsen, H.J.C.5
-
3
-
-
0001295503
-
Principal component analysis and long-time protein dynamics
-
Balsera, M. A., W. Wriggers, Y. Oono, and K. Schulten. 1996. Principal component analysis and long-time protein dynamics. J. Phys. Chem. 100:2567-2572.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2567-2572
-
-
Balsera, M.A.1
Wriggers, W.2
Oono, Y.3
Schulten, K.4
-
4
-
-
0030021471
-
Bio-molecular dynamics comes of age
-
Berendsen, H. J. C. 1996. Bio-molecular dynamics comes of age. Science. 271:954-955.
-
(1996)
Science
, vol.271
, pp. 954-955
-
-
Berendsen, H.J.C.1
-
5
-
-
0029633168
-
Gromacs - A message-passing parallel molecular-dynamics implementation
-
Berendsen, H. J. C., D. van der Spoel, and R. van Drunen. 1995. Gromacs - a message-passing parallel molecular-dynamics implementation. Comp. Phys. Comm. 91:43-56.
-
(1995)
Comp. Phys. Comm.
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
Van Der Spoel, D.2
Van Drunen, R.3
-
6
-
-
0017411710
-
The protein data bank: A computer based archival file for macromolecular structures
-
Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The protein data bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
7
-
-
0029024462
-
Mutagenesis and laue structures of enzyme intermediates: Isocitrate dehydrogenase
-
Bolduc, J. M., D. H. Dyer, W. G. Scott, P. Singer, R. M. Sweet, Jr., and B. L. Stoddard. 1995. Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenase. Science. 268:1312-1318.
-
(1995)
Science
, vol.268
, pp. 1312-1318
-
-
Bolduc, J.M.1
Dyer, D.H.2
Scott, W.G.3
Singer, P.4
Sweet R.M., Jr.5
Stoddard, B.L.6
-
9
-
-
0028912595
-
A sampling problem in molecular dynamics simulations of macromolecules
-
Clarage, J. B., T. Romo, B. K. Andrews, and B. M. Pettitt. 1995. A sampling problem in molecular dynamics simulations of macromolecules. Proc. Natl. Acad. Sci. USA. 92:3288-3292.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 3288-3292
-
-
Clarage, J.B.1
Romo, T.2
Andrews, B.K.3
Pettitt, B.M.4
-
10
-
-
0028958868
-
Flap opening in hiv-1 protease simulated by "actived" molecular dynamics
-
Collins, J. R., S. K. Burt, and J. W. Erickson. 1995. Flap opening in hiv-1 protease simulated by "actived" molecular dynamics. Nature Struct. Biol. 4:334-338.
-
(1995)
Nature Struct. Biol.
, vol.4
, pp. 334-338
-
-
Collins, J.R.1
Burt, S.K.2
Erickson, J.W.3
-
11
-
-
0029811307
-
An extended sampling of the configurational space of hpr from E. coli
-
de Groot, B., A. Amadei, R. Scheek, N. van Nuland, and H. Berendsen. 1996a. An extended sampling of the configurational space of hpr from E. coli. Proteins Struct. Funct. Genet. 26:314-322.
-
(1996)
Proteins Struct. Funct. Genet.
, vol.26
, pp. 314-322
-
-
Groot, B.1
Amadei, A.2
Scheek, R.3
Van Nuland, N.4
Berendsen, H.5
-
12
-
-
0029967692
-
Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin
-
de Groot, B. L., A. Amadei, D. M. F. van Aalten, and H. J. C. Berendsen. 1996b. Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. J. Biomol. Struct. Dyn. 13:741-751.
-
(1996)
J. Biomol. Struct. Dyn.
, vol.13
, pp. 741-751
-
-
De Groot, B.L.1
Amadei, A.2
Van Aalten, D.M.F.3
Berendsen, H.J.C.4
-
13
-
-
0015994218
-
Real-space refinement of the structure of hen egg-white lysozyme
-
Diamond, R. 1974. Real-space refinement of the structure of hen egg-white lysozyme. J. Mol. Biol. 82:371-391.
-
(1974)
J. Mol. Biol.
, vol.82
, pp. 371-391
-
-
Diamond, R.1
-
14
-
-
0025047629
-
A mutant t4 lysozyme displays 5 different crystal conformations
-
Faber, H. R., and B. W. Matthews. 1990. A mutant t4 lysozyme displays 5 different crystal conformations. Nature. 348:263-266.
-
(1990)
Nature
, vol.348
, pp. 263-266
-
-
Faber, H.R.1
Matthews, B.W.2
-
15
-
-
0000577041
-
Large-amplitude nonlinear motions in proteins
-
Garcia, A. E. 1992. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:2696-2699.
-
(1992)
Phys. Rev. Lett.
, vol.68
, pp. 2696-2699
-
-
Garcia, A.E.1
-
16
-
-
0031039399
-
Millisecond time-resolved laue crystallography: Structure of a protein photocycle intermediate
-
Genick, U. K., G. E. O. Borgstahl, N. Kingman, Z. Ren, C. Pradervand, P. Burke, V. Srajer, T. Teng, W. Schildkamp, D. E. McRee, K. Moffat, and E. D. Getzoff. 1997. Millisecond time-resolved laue crystallography: structure of a protein photocycle intermediate. Science. 275:1471-1475.
-
(1997)
Science
, vol.275
, pp. 1471-1475
-
-
Genick, U.K.1
Borgstahl, G.E.O.2
Kingman, N.3
Ren, Z.4
Pradervand, C.5
Burke, P.6
Srajer, V.7
Teng, T.8
Schildkamp, W.9
McRee, D.E.10
Moffat, K.11
Getzoff, E.D.12
-
17
-
-
33751156797
-
Protein dynamics in the bacteriorhodopsin photocycle - A nanosecond step-scan FTIR investigation of the kl to 1 transition
-
Hage, W., M. Kim, H. Frei, and R. A. Mathies. 1996. Protein dynamics in the bacteriorhodopsin photocycle - a nanosecond step-scan FTIR investigation of the kl to 1 transition. J. Phys. Chem. 100:16026-16033.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 16026-16033
-
-
Hage, W.1
Kim, M.2
Frei, H.3
Mathies, R.A.4
-
18
-
-
0028204451
-
Solution structure and dynamics of ras-p21-gdp determined by heteronuclear three- and four-dimensional NMR spectroscopy
-
Kraulis, P. J., P. J. Domaille, S. L. Campbell-Burk, T. van Aken, and E. D. Laue. 1994. Solution structure and dynamics of ras-p21-gdp determined by heteronuclear three- and four-dimensional NMR spectroscopy. Biochemistry. 33:3515-3531.
-
(1994)
Biochemistry
, vol.33
, pp. 3515-3531
-
-
Kraulis, P.J.1
Domaille, P.J.2
Campbell-Burk, S.L.3
Van Aken, T.4
Laue, E.D.5
-
19
-
-
0025787958
-
Insight into the conformational dynamics of specific regions of porcine pancreatic phospholipase a2 from a time-resolved fluorescence study of a genetically inserted single tryptophan
-
Kuipers, O. P., M. Vincent, J.-C. Brochon, H. M. Verheij, G. H. de Haas, and J. Gallay. 1991. Insight into the conformational dynamics of specific regions of porcine pancreatic phospholipase a2 from a time-resolved fluorescence study of a genetically inserted single tryptophan. Biochemistry. 30:8771-8785.
-
(1991)
Biochemistry
, vol.30
, pp. 8771-8785
-
-
Kuipers, O.P.1
Vincent, M.2
Brochon, J.-C.3
Verheij, H.M.4
De Haas, G.H.5
Gallay, J.6
-
20
-
-
0027520474
-
Structure and dynamics of barnase complexed with 3′-GMP studied by NMR spectroscopy
-
Meiering, E. M., M. Bycroft, M. J. Lubienski, and A. R. Fersht. 1993. Structure and dynamics of barnase complexed with 3′-GMP studied by NMR spectroscopy. Biochemistry. 32:10975-10987.
-
(1993)
Biochemistry
, vol.32
, pp. 10975-10987
-
-
Meiering, E.M.1
Bycroft, M.2
Lubienski, M.J.3
Fersht, A.R.4
-
21
-
-
0030979309
-
Comparison of RAS-p21 bound to GDP and GTP: Differences in protein and ligand dynamics
-
Mello, L. V., D. M. F. van Aalten, and J. B. C. Findlay. 1997. Comparison of RAS-p21 bound to GDP and GTP: differences in protein and ligand dynamics. Prot. Eng. 10:381-387.
-
(1997)
Prot. Eng.
, vol.10
, pp. 381-387
-
-
Mello, L.V.1
Van Aalten, D.M.F.2
Findlay, J.B.C.3
-
22
-
-
0024528771
-
Time-resolved macromolecular crystallography
-
Moffat, K. 1989. Time-resolved macromolecular crystallography. Annu. Rev. Biophys. Biophys. Chem. 18:309-332.
-
(1989)
Annu. Rev. Biophys. Biophys. Chem.
, vol.18
, pp. 309-332
-
-
Moffat, K.1
-
23
-
-
0028174289
-
Crystal structures of E. coli aspartate aminotransferase in two conformations
-
Moser, M., U. Sauder, and J. N. Jansonius. 1994. Crystal structures of E. coli aspartate aminotransferase in two conformations. J. Mol. Biol. 239:285-305.
-
(1994)
J. Mol. Biol.
, vol.239
, pp. 285-305
-
-
Moser, M.1
Sauder, U.2
Jansonius, J.N.3
-
24
-
-
0029159748
-
Rigid domains in proteins: An algorithmic approach to their identification
-
Nichols, W. L., G. D. Rose, L. F. T. Eyck, and B. H. Zimm. 1995. Rigid domains in proteins: an algorithmic approach to their identification. Proteins Struct. Funct. Genet. 23:38-48.
-
(1995)
Proteins Struct. Funct. Genet.
, vol.23
, pp. 38-48
-
-
Nichols, W.L.1
Rose, G.D.2
Eyck, L.F.T.3
Zimm, B.H.4
-
25
-
-
0028921302
-
Flexibility and function in hiv-1 protease
-
Nicholson, L. K., T. Yamazaki, D. A. Torchia, S. Grzesiek, A. Bax, S. J. Stahl, J. D. Kaufman, P. T. Wingfield, P. Y. S. Lam, P. K. Jadhav, N. Hodge, P. J. Domaille, and C.-H. Chang. 1995. Flexibility and function in hiv-1 protease. Nature Struct. Biol. 4:274-280.
-
(1995)
Nature Struct. Biol.
, vol.4
, pp. 274-280
-
-
Nicholson, L.K.1
Yamazaki, T.2
Torchia, D.A.3
Grzesiek, S.4
Bax, A.5
Stahl, S.J.6
Kaufman, J.D.7
Wingfield, P.T.8
Lam, P.Y.S.9
Jadhav, P.K.10
Hodge, N.11
Domaille, P.J.12
Chang, C.-H.13
-
26
-
-
0000421878
-
Nature of forces between large molecules of biological interest
-
Pauling, L. 1948. Nature of forces between large molecules of biological interest. Nature. 161:707-709.
-
(1948)
Nature
, vol.161
, pp. 707-709
-
-
Pauling, L.1
-
27
-
-
0025037796
-
Comparison of the dynamics of myoglobin in different crystal forms
-
Phillips, G. N. 1990. Comparison of the dynamics of myoglobin in different crystal forms. Biophys. J. 57:381-383.
-
(1990)
Biophys. J.
, vol.57
, pp. 381-383
-
-
Phillips, G.N.1
-
28
-
-
0026449003
-
Picosecond phase grating spectroscopy of hemoglobin and myoglobin: Energetics and dynamics of global protein motion
-
Richard, L., L. Genberg, J. Deak, H.-L. Chiu, and R. J. D. Miller. 1992. Picosecond phase grating spectroscopy of hemoglobin and myoglobin: energetics and dynamics of global protein motion. Biochemistry. 31: 10703-10715.
-
(1992)
Biochemistry
, vol.31
, pp. 10703-10715
-
-
Richard, L.1
Genberg, L.2
Deak, J.3
Chiu, H.-L.4
Miller, R.J.D.5
-
29
-
-
0029113863
-
Automatic identification of discrete substrates in proteins: Singular value decomposition analysis of time-averaged crystallographic refinements
-
Romo, T. D., J. B. Clarage, D. C. Sorensen, and G. N. Phillips. 1995. Automatic identification of discrete substrates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements. Proteins Struct. Funct. Genet. 22:311-321.
-
(1995)
Proteins Struct. Funct. Genet.
, vol.22
, pp. 311-321
-
-
Romo, T.D.1
Clarage, J.B.2
Sorensen, D.C.3
Phillips, G.N.4
-
30
-
-
0029162947
-
Comparison of MD simulations and NMR experiments from hen lysozyme - Analysis of local fluctuations, cooperative motions and global changes
-
Smith, L. J., A. E. Mark, C. M. Dobson, and W. F. van Gunsteren. 1995. Comparison of MD simulations and NMR experiments from hen lysozyme - analysis of local fluctuations, cooperative motions and global changes. Biochemistry. 34:10918-10931.
-
(1995)
Biochemistry
, vol.34
, pp. 10918-10931
-
-
Smith, L.J.1
Mark, A.E.2
Dobson, C.M.3
Van Gunsteren, W.F.4
-
31
-
-
0028027596
-
GTPase mechanism of g-proteins from the 1.7 angstrom crystal structure of transducin α-GDP
-
Sondek, J., D. G. Lambright, J. P. Noel, H. E. Hamm, and P. B. Sigler. 1994. GTPase mechanism of g-proteins from the 1.7 angstrom crystal structure of transducin α-GDP. Nature. 372:276-279.
-
(1994)
Nature
, vol.372
, pp. 276-279
-
-
Sondek, J.1
Lambright, D.G.2
Noel, J.P.3
Hamm, H.E.4
Sigler, P.B.5
-
32
-
-
10544231457
-
Photolysis of the carbon monoxide complex of myoglobin - Nanosecond time-resolved crystallography
-
Srajer, V., T. Y. Teng, T. Ursby, C. Pradervand, Z. Ren, S. Adachi, W. Schildkamp, D. Bourgeois, M. Wulff, and K. Moffat. 1996. Photolysis of the carbon monoxide complex of myoglobin - nanosecond time-resolved crystallography. Science. 274:1726-1729.
-
(1996)
Science
, vol.274
, pp. 1726-1729
-
-
Srajer, V.1
Teng, T.Y.2
Ursby, T.3
Pradervand, C.4
Ren, Z.5
Adachi, S.6
Schildkamp, W.7
Bourgeois, D.8
Wulff, M.9
Moffat, K.10
-
33
-
-
0027968068
-
Clustal-w -improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal-w -improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
34
-
-
0030043196
-
A comparison of structural and dynamic properties of different simulation methods applied to sh3
-
van Aalten, D. M. F., A. Amadei, R. Bywater, J. B. C. Findlay, H. J. C. Berendsen, C. Sander, and P. F. W. Stouten. 1996a. A comparison of structural and dynamic properties of different simulation methods applied to sh3. Biophys. J. 70:684-692.
-
(1996)
Biophys. J.
, vol.70
, pp. 684-692
-
-
Van Aalten, D.M.F.1
Amadei, A.2
Bywater, R.3
Findlay, J.B.C.4
Berendsen, H.J.C.5
Sander, C.6
Stouten, P.F.W.7
-
35
-
-
0029075795
-
The essential dynamics of thermolysin - Confirmation of hinge-bending motion and comparison of simulations in vacuum and water
-
van Aalten, D. M. F., A. Amadei, G. Vriend, A. B. M. Linssen, G. Venema, H. J. C. Berendsen, and V. G. H. Eijsink. 1995. The essential dynamics of thermolysin - confirmation of hinge-bending motion and comparison of simulations in vacuum and water. Proteins. 22:45-54.
-
(1995)
Proteins
, vol.22
, pp. 45-54
-
-
Van Aalten, D.M.F.1
Amadei, A.2
Vriend, G.3
Linssen, A.B.M.4
Venema, G.5
Berendsen, H.J.C.6
Eijsink, V.G.H.7
-
36
-
-
0029586726
-
Essential dynamics of the cellular retinol binding protein -evidence for ligand induced conformational changes
-
van Aalten, D. M. F., J. B. C. Findlay, A. Amadei, and H. J. C. Berendsen. 1996b. Essential dynamics of the cellular retinol binding protein -evidence for ligand induced conformational changes. Protein Eng. 8: 1129-1135.
-
(1996)
Protein Eng.
, vol.8
, pp. 1129-1135
-
-
Van Aalten, D.M.F.1
Findlay, J.B.C.2
Amadei, A.3
Berendsen, H.J.C.4
-
37
-
-
0342547217
-
Engineering protein mechanics: Inhibition of concerted motions of the cellular retinol binding protein by site directed mutagenesis
-
in press
-
van Aalten, D. M. F., P. C. Jones, M. de Sousa, and J. B. C. Findlay. 1996c. Engineering protein mechanics: inhibition of concerted motions of the cellular retinol binding protein by site directed mutagenesis. Protein Eng. (in press).
-
(1996)
Protein Eng.
-
-
Van Aalten, D.M.F.1
Jones, P.C.2
De Sousa, M.3
Findlay, J.B.C.4
-
38
-
-
0003916606
-
-
Nijenborgh 4, 9747 AG Groningen, The Netherlands
-
van der Spoel, D., H. J. C. Berendsen, A. R. van Buuren, E. Apol, P. J. Meulenhoff, A. L. T. M. Sijbers, and R. van Drunen. 1995. Gromacs User Manual. Nijenborgh 4, 9747 AG Groningen, The Netherlands (Internet: http://rugmd0.chem.rug.nl/~gmx).
-
(1995)
Gromacs User Manual
-
-
Van Der Spoel, D.1
Berendsen, H.J.C.2
Van Buuren, A.R.3
Apol, E.4
Meulenhoff, P.J.5
Sijbers, A.L.T.M.6
Van Drunen, R.7
-
39
-
-
0004146515
-
-
BIOMOS, Biomolecular Software, Laboratory of Physical Chemistry, University of Groningen, Groningen, The Netherlands
-
van Gunsteren, W. F., and H. J. C. Berendsen. 1987. Gromos Manual. BIOMOS, Biomolecular Software, Laboratory of Physical Chemistry, University of Groningen, Groningen, The Netherlands.
-
(1987)
Gromos Manual
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
40
-
-
0029644728
-
Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
-
Vonrhein, C., G. J. Schlauderer, and G. E. Schulz. 1995. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure. 3:483-490.
-
(1995)
Structure
, vol.3
, pp. 483-490
-
-
Vonrhein, C.1
Schlauderer, G.J.2
Schulz, G.E.3
-
41
-
-
0028092978
-
A possible route for the release of fatty acid from fatty acid binding protein
-
Zanotti, G., L. Feltre, and P. Spadon. 1994. A possible route for the release of fatty acid from fatty acid binding protein. Biochem. J. 301:459-463.
-
(1994)
Biochem. J.
, vol.301
, pp. 459-463
-
-
Zanotti, G.1
Feltre, L.2
Spadon, P.3
-
42
-
-
0029150760
-
Protein flexibility and adaptability seen in 25 crystal forms of t4 lysozyme
-
Zhang, X., J. A. Wozniak, and B. W. Matthews. 1995. Protein flexibility and adaptability seen in 25 crystal forms of t4 lysozyme. J. Mol. Biol. 250:527-552.
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 527-552
-
-
Zhang, X.1
Wozniak, J.A.2
Matthews, B.W.3
|