-
1
-
-
0027293559
-
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy
-
Brünger, A.T. & Nilges, M. (1993). Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy. Quart. Rev. Biophys. 26, 49-125.
-
(1993)
Quart. Rev. Biophys.
, vol.26
, pp. 49-125
-
-
Brünger, A.T.1
Nilges, M.2
-
2
-
-
0024791275
-
Distance geometry
-
Kuntz, I.D., Thomason, J.F., & Oshiro, C.M. (1989). Distance geometry. Methods. Enzymol. 177, 159-204.
-
(1989)
Methods. Enzymol.
, vol.177
, pp. 159-204
-
-
Kuntz, I.D.1
Thomason, J.F.2
Oshiro, C.M.3
-
3
-
-
0025932859
-
An evaluation of computational strategies for use in the determination of protein-structure from distance constraints obtained by nuclear magnetic resonance
-
Havel, T.F. (1991). An evaluation of computational strategies for use in the determination of protein-structure from distance constraints obtained by nuclear magnetic resonance. Prog. Biophys. Mol. Biol. 56, 43-78.
-
(1991)
Prog. Biophys. Mol. Biol.
, vol.56
, pp. 43-78
-
-
Havel, T.F.1
-
4
-
-
0023339433
-
Distance geometry and related methods for protein structure determination from NMR data
-
Braun, W. (1987). Distance geometry and related methods for protein structure determination from NMR data. Quart. Rev. Biophys. 19, 115-157.
-
(1987)
Quart. Rev. Biophys.
, vol.19
, pp. 115-157
-
-
Braun, W.1
-
5
-
-
0026259488
-
Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints
-
Güntert, P. & Wüthrich, K. (1991). Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Biomol. NMR 1, 447-456.
-
(1991)
J. Biomol. NMR
, vol.1
, pp. 447-456
-
-
Güntert, P.1
Wüthrich, K.2
-
6
-
-
0021095856
-
Protein folding by restrained energy minimization and molecular dynamics
-
Levitt, M. (1983). Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170, 723-764.
-
(1983)
J. Mol. Biol.
, vol.170
, pp. 723-764
-
-
Levitt, M.1
-
7
-
-
0022419169
-
A protein structure from nuclear magnetic resonance data. Lac repressor headpiece
-
Kaptein, R., Zuiderweg, E. R.P., Scheek, R.M., Boelens, R. & Van Gunsteren, W.A. (1985). A protein structure from nuclear magnetic resonance data. Lac repressor headpiece. J. Mol. Biol. 182, 179-182.
-
(1985)
J. Mol. Biol.
, vol.182
, pp. 179-182
-
-
Kaptein, R.1
Zuiderweg, E.R.P.2
Scheek, R.M.3
Boelens, R.4
Van Gunsteren, W.A.5
-
9
-
-
0000870109
-
Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin
-
Brünger, A.T., Clore, G.M., Gronenborn, A.M. & Karplus, M. (1986). Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl Acad Sci. USA 83, 3801-3805.
-
(1986)
Proc. Natl Acad Sci. USA
, vol.83
, pp. 3801-3805
-
-
Brünger, A.T.1
Clore, G.M.2
Gronenborn, A.M.3
Karplus, M.4
-
10
-
-
0024285896
-
Determination of three-dimensional structures of proteins by hybrid distance geometry-dynamical simulated annealing calculations
-
Nilges, M., Clore, G.M. & Gronenborn, A.M. (1988). Determination of three-dimensional structures of proteins by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229, 317-324.
-
(1988)
FEBS Lett.
, vol.229
, pp. 317-324
-
-
Nilges, M.1
Clore, G.M.2
Gronenborn, A.M.3
-
11
-
-
0023998438
-
Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2
-
Nilges, M., Gronenborn, A.M., Brünger, A.T. & Clore, G.M. (1988). Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27-38.
-
(1988)
Protein Eng.
, vol.2
, pp. 27-38
-
-
Nilges, M.1
Gronenborn, A.M.2
Brünger, A.T.3
Clore, G.M.4
-
12
-
-
0023732144
-
Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms: Avoiding problems associated with folding
-
Nilges, M., Clore, G.M. & Gronenborn, A.M. (1988). Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms: avoiding problems associated with folding. FEBS Lett. 239, 129-136.
-
(1988)
FEBS Lett.
, vol.239
, pp. 129-136
-
-
Nilges, M.1
Clore, G.M.2
Gronenborn, A.M.3
-
13
-
-
0001708879
-
Sampling properties of simulated annealing and distance geometry
-
vol. 225 of NATO ASI Series. (Hoch, J.C., Poulsen, F.M., & Redfield, C., eds), Plenum, New York
-
Nilges, M., Kuszewski, J. & Brünger, A.T. (1991). Sampling properties of simulated annealing and distance geometry. In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, vol. 225 of NATO ASI Series. (Hoch, J.C., Poulsen, F.M., & Redfield, C., eds), pp. 451-455, Plenum, New York.
-
(1991)
Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy
, pp. 451-455
-
-
Nilges, M.1
Kuszewski, J.2
Brünger, A.T.3
-
15
-
-
0027501685
-
A reduced representation of proteins for use in restraint satisfaction calculations
-
Herzyk, P. & Hubbard, R.E. (1993). A reduced representation of proteins for use in restraint satisfaction calculations. Proteins 17, 310-324.
-
(1993)
Proteins
, vol.17
, pp. 310-324
-
-
Herzyk, P.1
Hubbard, R.E.2
-
16
-
-
0346050341
-
A method for determining overall protein fold from NMR distance restraints
-
Hoch, J.C. & Stern, A.S. (1992). A method for determining overall protein fold from NMR distance restraints. J. Biomol. NMR 2, 535-543.
-
(1992)
J. Biomol. NMR
, vol.2
, pp. 535-543
-
-
Hoch, J.C.1
Stern, A.S.2
-
17
-
-
0027383637
-
1H NMR
-
1H NMR. Proteins 17, 297-309.
-
(1993)
Proteins
, vol.17
, pp. 297-309
-
-
Nilges, M.1
-
18
-
-
0028907436
-
Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE cross-peaks and disulphide connectivities
-
Nilges, M. (1995). Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE cross-peaks and disulphide connectivities. J. Mol. Biol. 245, 645-660.
-
(1995)
J. Mol. Biol.
, vol.245
, pp. 645-660
-
-
Nilges, M.1
-
19
-
-
0027141511
-
A structure refinement method based on molecular dynamics in four spatial dimensions
-
Van Schaik, R.C., Berendsen, H.J., Torda, A.E. & Van Gunsteren, W.F. (1993). A structure refinement method based on molecular dynamics in four spatial dimensions. J. Mol. Biol. 234, 751-762.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 751-762
-
-
Van Schaik, R.C.1
Berendsen, H.J.2
Torda, A.E.3
Van Gunsteren, W.F.4
-
20
-
-
0027347355
-
Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties
-
Nakai, T., Kidera, A. & Nakamura, H. (1993). Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties. J. Biomol. NMR 3, 19-40.
-
(1993)
J. Biomol. NMR
, vol.3
, pp. 19-40
-
-
Nakai, T.1
Kidera, A.2
Nakamura, H.3
-
21
-
-
0028070557
-
Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement
-
Rice, L.M. & Brünger, A.T. (1994). Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19, 277-290.
-
(1994)
Proteins
, vol.19
, pp. 277-290
-
-
Rice, L.M.1
Brünger, A.T.2
-
22
-
-
0030621858
-
Torsion angle molecular dynamics as a new efficient tool for NMR structure calculation
-
Stein, E.G., Rice, L.M. & Brünger, A.T. (1997). Torsion angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 124, 154-164.
-
(1997)
J. Magn. Reson.
, vol.124
, pp. 154-164
-
-
Stein, E.G.1
Rice, L.M.2
Brünger, A.T.3
-
23
-
-
0029610793
-
Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry
-
Mumenthaler, C. & Braun, W. (1996). Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. J. Mol. Biol. 254, 465-480.
-
(1996)
J. Mol. Biol.
, vol.254
, pp. 465-480
-
-
Mumenthaler, C.1
Braun, W.2
-
24
-
-
0000194538
-
The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination
-
Güntert, P., Berndt, K.D. & Wüthrich, K. (1993). The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. J. Biomol. NMR 3, 601-606.
-
(1993)
J. Biomol. NMR
, vol.3
, pp. 601-606
-
-
Güntert, P.1
Berndt, K.D.2
Wüthrich, K.3
-
25
-
-
0027929299
-
A computer-based protocol for semiautomated assignments and 3D structure determination of proteins
-
Meadows, R.P., Olejniczak, E.T. & Fesik, S.W. (1994). A computer-based protocol for semiautomated assignments and 3D structure determination of proteins. J. Biomol. NMR 4, 79-96.
-
(1994)
J. Biomol. NMR
, vol.4
, pp. 79-96
-
-
Meadows, R.P.1
Olejniczak, E.T.2
Fesik, S.W.3
-
26
-
-
0000081715
-
Approche directe de la détermination de structures moléculaires à partir de l'effet Overhauser nucléaire
-
[Title translation: Direct approach to the determination of molecular structure from the nuclear Overhauser effect]
-
Malliavin, T.E., Rouh, A., Delsuc, M.A. & Lallemand, J.-Y. (1992). Approche directe de la détermination de structures moléculaires à partir de l'effet Overhauser nucléaire. C.R. Acad. Sci. Paris 315, 653-659. [Title translation: Direct approach to the determination of molecular structure from the nuclear Overhauser effect]
-
(1992)
C.R. Acad. Sci. Paris
, vol.315
, pp. 653-659
-
-
Malliavin, T.E.1
Rouh, A.2
Delsuc, M.A.3
Lallemand, J.-Y.4
-
27
-
-
0027463598
-
Application of distance geometry to the proton assignment problem
-
Oshiro, C.M. & Kuntz, I.D. (1993). Application of distance geometry to the proton assignment problem. Biopolymers 33, 107-115.
-
(1993)
Biopolymers
, vol.33
, pp. 107-115
-
-
Oshiro, C.M.1
Kuntz, I.D.2
-
28
-
-
0028029630
-
15N separated NOE data: A novel real space ab initio approach
-
15N separated NOE data: a novel real space ab initio approach. J. Mol. Biol. 243, 696-718.
-
(1994)
J. Mol. Biol.
, vol.243
, pp. 696-718
-
-
Kraulis, P.1
-
29
-
-
0025894164
-
Relaxation matrix refinement of the solution structure of squash trypsin inhibitor
-
Nilges, M., Habazettl, J., Brünger, A.T. & Holak, T.A. (1991). Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. J. Mol. Biol. 219, 499-510.
-
(1991)
J. Mol. Biol.
, vol.219
, pp. 499-510
-
-
Nilges, M.1
Habazettl, J.2
Brünger, A.T.3
Holak, T.A.4
-
30
-
-
0029058994
-
Structure of the dsRNA binding domain of E. coli RNase III
-
Kharrat, A., Macias, M.J., Gibson, T., Nilges, M. & Pastore, A. (1995). Structure of the dsRNA binding domain of E. coli RNase III. EMBO J. 14, 3572-3584.
-
(1995)
EMBO J.
, vol.14
, pp. 3572-3584
-
-
Kharrat, A.1
Macias, M.J.2
Gibson, T.3
Nilges, M.4
Pastore, A.5
-
31
-
-
33645652870
-
Automated assignment of ambiguous crosspeaks in symmetric dimers
-
Nilges, M. & Brünger, A.T. (1991). Automated assignment of ambiguous crosspeaks in symmetric dimers. J. Cell. Biochem. 15G, CG 422.
-
(1991)
J. Cell. Biochem.
, vol.15 G
-
-
Nilges, M.1
Brünger, A.T.2
-
32
-
-
0028216128
-
The solution structure of the Tyr41→His mutant of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13
-
Folkers, P.J.M., Nilges, M., Folmer, R.H.A., Konings, R.N.H. & Hilbers, C.W. (1994). The solution structure of the Tyr41→His mutant of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13. J. Mol. Biol. 236, 229-246.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 229-246
-
-
Folkers, P.J.M.1
Nilges, M.2
Folmer, R.H.A.3
Konings, R.N.H.4
Hilbers, C.W.5
-
33
-
-
84970061891
-
Solution structure of the tetrameric minimum transforming domain of p53
-
Lee, W., Harvey, T.S., Yin, Y., Yau, P., Litchfield, D. & Arrowsmith, C.H. (1994). Solution structure of the tetrameric minimum transforming domain of p53. Nat Struct. Biol. 1, 877-890.
-
(1994)
Nat Struct. Biol.
, vol.1
, pp. 877-890
-
-
Lee, W.1
Harvey, T.S.2
Yin, Y.3
Yau, P.4
Litchfield, D.5
Arrowsmith, C.H.6
-
34
-
-
0029000758
-
Solution structure of a cellulose-binding domain from cellulomonas fimi by nuclear magnetic resonance spectroscopy
-
Xu, G.Y., et al., & Harvey, T.S. (1995). Solution structure of a cellulose-binding domain from cellulomonas fimi by nuclear magnetic resonance spectroscopy. Biochemistry 34, 6993-7009.
-
(1995)
Biochemistry
, vol.34
, pp. 6993-7009
-
-
Xu, G.Y.1
Harvey, T.S.2
-
35
-
-
0028066921
-
A model of the complex between single-stranded DNA and the single-stranded DNA binding protein encoded by gene V of filamentous bacteriophage M13
-
Folmer, R.H.A., Nilges, M., Folkers, P.J.M., Konings, R.N.H. & Hilbers, C.W. (1995). A model of the complex between single-stranded DNA and the single-stranded DNA binding protein encoded by gene V of filamentous bacteriophage M13. J. Mol. Biol. 240, 341-357.
-
(1995)
J. Mol. Biol.
, vol.240
, pp. 341-357
-
-
Folmer, R.H.A.1
Nilges, M.2
Folkers, P.J.M.3
Konings, R.N.H.4
Hilbers, C.W.5
-
36
-
-
0029088520
-
Solution structure of the single-stranded DNA binding protein of bacteriophage Pf3
-
Folmer, R.H.A., Nilges, M., Konings, R.N.H. & Hilbers, C.W. (1995). Solution structure of the single-stranded DNA binding protein of bacteriophage Pf3. EMBO J. 14, 4132-4142.
-
(1995)
EMBO J.
, vol.14
, pp. 4132-4142
-
-
Folmer, R.H.A.1
Nilges, M.2
Konings, R.N.H.3
Hilbers, C.W.4
-
38
-
-
0011871162
-
Distinguishing symmetry-related intramolecular and intermolecular nuclear overhauser effects in a protein by asymmetric isotopic labelling
-
Weiss, M.A. (1990). Distinguishing symmetry-related intramolecular and intermolecular nuclear overhauser effects in a protein by asymmetric isotopic labelling. J. Magn. Reson. 86, 626-632.
-
(1990)
J. Magn. Reson.
, vol.86
, pp. 626-632
-
-
Weiss, M.A.1
-
39
-
-
0000711201
-
Overcoming the ambiguity problem encountered in the analysis of nuclear magnetic resonance spectra of symmetric dimer proteins
-
Folkers, P.J.M., Folmer, R.H.A., Konings, R.N.H. & Hilbers, C.W. (1993). Overcoming the ambiguity problem encountered in the analysis of nuclear magnetic resonance spectra of symmetric dimer proteins. J. Am. Chem. Soc. 115, 3798-3799.
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 3798-3799
-
-
Folkers, P.J.M.1
Folmer, R.H.A.2
Konings, R.N.H.3
Hilbers, C.W.4
-
40
-
-
0001441922
-
Calculation of symmetric multimer structures from NMR data using a priori knowledge of the monomer structure, co-monomer restraints, and interface mapping: The case of leucine zippers
-
O'Donoghue, S.I., King, G.F. & Nilges, M. (1996). Calculation of symmetric multimer structures from NMR data using a priori knowledge of the monomer structure, co-monomer restraints, and interface mapping: the case of leucine zippers. J. Biomol. NMR 8, 193-206.
-
(1996)
J. Biomol. NMR
, vol.8
, pp. 193-206
-
-
O'Donoghue, S.I.1
King, G.F.2
Nilges, M.3
-
41
-
-
0028238582
-
Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin
-
Haenggi, G. & Braun, W. (1994). Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin. FEBS Lett. 344, 147-153.
-
(1994)
FEBS Lett.
, vol.344
, pp. 147-153
-
-
Haenggi, G.1
Braun, W.2
-
42
-
-
0031566434
-
Automated NOESY interpretation with ambiguous distance restraints: The refined NMR solution structure of the pleckstrin homology domain from β-spectrin
-
Nilges, M., Macias, M.J., O'Donoghue, S.I. & Oschkinat, H. (1997). Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin. J. Mol. Biol. 269, 408-422.
-
(1997)
J. Mol. Biol.
, vol.269
, pp. 408-422
-
-
Nilges, M.1
Macias, M.J.2
O'Donoghue, S.I.3
Oschkinat, H.4
-
43
-
-
0029988528
-
Three-dimensional structure and stability of the KH domain: Molecular insights into the fragile X syndrome
-
Musco, G., et al., & Pastore, A. (1996). Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. Cell 85, 237-246.
-
(1996)
Cell
, vol.85
, pp. 237-246
-
-
Musco, G.1
Pastore, A.2
-
44
-
-
0029096888
-
Structure of the binding site for inositol phosphates in a PH domain
-
Hyvönen, M., Macias, M.J., Nilges, M., Oschkinat, H., Saraste, M. & Wilmanns, M. (1995). Structure of the binding site for inositol phosphates in a PH domain. EMBO J. 14, 4676-4685.
-
(1995)
EMBO J.
, vol.14
, pp. 4676-4685
-
-
Hyvönen, M.1
Macias, M.J.2
Nilges, M.3
Oschkinat, H.4
Saraste, M.5
Wilmanns, M.6
-
45
-
-
0027542118
-
Quality control of protein models: Directional atomic contact analysis
-
Vriend, G. & Sander, C. (1993). Quality control of protein models: directional atomic contact analysis. J. Appl. Crystallogr. 26, 47-60.
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 47-60
-
-
Vriend, G.1
Sander, C.2
-
46
-
-
0026655361
-
Stereochemical quality of protein structure co-ordinates
-
Morris, A.L., MacArthur, M.W., Hutchinson, E.G. & Thornton, J. (1992). Stereochemical quality of protein structure co-ordinates. Proteins 12, 345-364.
-
(1992)
Proteins
, vol.12
, pp. 345-364
-
-
Morris, A.L.1
MacArthur, M.W.2
Hutchinson, E.G.3
Thornton, J.4
-
47
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl, M.J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins 17, 355-362.
-
(1993)
Proteins
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
48
-
-
33645671280
-
A distance geometry-based approach for docking conformationally flexible molecules from 2D or 3D-chemical data-bases
-
p. CINF 28, New York
-
Blaney, J. (1991). A distance geometry-based approach for docking conformationally flexible molecules from 2D or 3D-chemical data-bases. In Abstracts of Papers of the American Chemical Society, Fourth Chemical Congress of North America, vol. 202, p. CINF 28, New York.
-
(1991)
Abstracts of Papers of the American Chemical Society, Fourth Chemical Congress of North America
, vol.202
-
-
Blaney, J.1
-
49
-
-
0023140814
-
Crystallographic R factor refinement by molecular dynamics
-
Brünger, A.T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science 235, 458-460.
-
(1987)
Science
, vol.235
, pp. 458-460
-
-
Brünger, A.T.1
Kuriyan, J.2
Karplus, M.3
|