-
1
-
-
0023140814
-
Crystallographic R factor refinement by molecular dynamics
-
Brünger AT, Kuriyan J, Karplus M. Crystallographic R factor refinement by molecular dynamics. Science 1987;235:458-460.
-
(1987)
Science
, vol.235
, pp. 458-460
-
-
Brünger, A.T.1
Kuriyan, J.2
Karplus, M.3
-
2
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and molecular dynamics calculations
-
Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and molecular dynamics calculations. J Comp Chem 1983;4:187-217.
-
(1983)
J Comp Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
4
-
-
0028070557
-
Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement
-
Rice LM, Brünger AT. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 1994;19:277-290.
-
(1994)
Proteins
, vol.19
, pp. 277-290
-
-
Rice, L.M.1
Brünger, A.T.2
-
5
-
-
0030621858
-
Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation
-
Stein EG, Rice LM, Brünger AT. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J Magn Reson 1997;124:154-164.
-
(1997)
J Magn Reson
, vol.124
, pp. 154-164
-
-
Stein, E.G.1
Rice, L.M.2
Brünger, A.T.3
-
6
-
-
0030038545
-
Direct observation of protein solvation and discrete disorder with experimental phases
-
Burling FT, Weis WI, Flaherty KM, Brünger AT. Direct observation of protein solvation and discrete disorder with experimental phases. Science 1995;271:72-77.
-
(1995)
Science
, vol.271
, pp. 72-77
-
-
Burling, F.T.1
Weis, W.I.2
Flaherty, K.M.3
Brünger, A.T.4
-
7
-
-
0028172551
-
Protein hydration observed by x-ray diffraction:Solvation properties of penicillopepsin and neuraminidase crystal structures
-
Jiang J-A, Brünger AT. Protein hydration observed by x-ray diffraction:solvation properties of penicillopepsin and neuraminidase crystal structures. J Mol Biol 1994;243:100-115.
-
(1994)
J Mol Biol
, vol.243
, pp. 100-115
-
-
Jiang, J.-A.1
Brünger, A.T.2
-
8
-
-
0028432974
-
The impact of direct refinement against three-bond HN-CaH coupling constants on protein structure determination by NMR
-
Garret DS, Kuszewski J, Hancock TJ, Lodi PJ, Vuister GW, Gronenborn AM, Clore GM. The impact of direct refinement against three-bond HN-CaH coupling constants on protein structure determination by NMR. J Magn Reson 1994;B104:99-103.
-
(1994)
J Magn Reson
, vol.B104
, pp. 99-103
-
-
Garret, D.S.1
Kuszewski, J.2
Hancock, T.J.3
Lodi, P.J.4
Vuister, G.W.5
Gronenborn, A.M.6
Clore, G.M.7
-
9
-
-
0029314335
-
The impact of direct refinement against proton chemical shifts in protein structure determination by NMR
-
Kuszewski J, Gronenborn AM, Clore GM. The impact of direct refinement against proton chemical shifts in protein structure determination by NMR. J Magn Reson 1995;B107:293-297.
-
(1995)
J Magn Reson
, vol.B107
, pp. 293-297
-
-
Kuszewski, J.1
Gronenborn, A.M.2
Clore, G.M.3
-
10
-
-
0029202363
-
The impact of direct refinement against 13Cα and 13Cβ chemical shifts on protein structure determination by NMR
-
Kuszewski J, Qin J, Gronenborn AM, Clore GM. The impact of direct refinement against 13Cα and 13Cβ chemical shifts on protein structure determination by NMR. J Magn Reson 1995; B106:92-96.
-
(1995)
J Magn Reson
, vol.B106
, pp. 92-96
-
-
Kuszewski, J.1
Qin, J.2
Gronenborn, A.M.3
Clore, G.M.4
-
11
-
-
0000649842
-
Improved structure refinement through maximum likelihood
-
Pannu NS, Read RJ. Improved structure refinement through maximum likelihood. Acta Crystallogr 1996;A52:659-668.
-
(1996)
Acta Crystallogr
, vol.A52
, pp. 659-668
-
-
Pannu, N.S.1
Read, R.J.2
-
12
-
-
0030924992
-
Refinement of macromolecular structures by the maximum-likelihood method
-
Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr 1997;D53:240-255.
-
(1997)
Acta Crystallogr
, vol.D53
, pp. 240-255
-
-
Murshudov, G.N.1
Vagin, A.A.2
Dodson, E.J.3
-
13
-
-
0001941113
-
Maximum-likelihood refinement of incomplete models with BUSTEr+TNT
-
Macromolecular Refinement Bailey S, Dodson EJ, editors. January 5-6.
-
Bricogne G, Irwin JJ. maximum-likelihood refinement of incomplete models with BUSTER+TNT. In: Bailey S, Dodson EJ, editors. Macromolecular refinement, Proceedings of the CCP4 Study Weekend at Chester College, January 5-6. 1996:85-92.
-
(1996)
Proceedings of the CCP4 Study Weekend at Chester College
, pp. 85-92
-
-
Bricogne, G.1
Irwin, J.J.2
-
14
-
-
0030986177
-
Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement
-
Adams PD, Pannu NS , Read RJ, Brünger AT. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc Natl Acad Sci USA 1997;94:5018-5023.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 5018-5023
-
-
Adams, P.D.1
Pannu, N.S.2
Read, R.J.3
Brünger, A.T.4
-
15
-
-
0032212015
-
Incorporation of prior phase probability information strengthens maximum likelihood structural refinement
-
Pannu NS, Murshudov GN, Dodson EJ, Read R. Incorporation of prior phase probability information strengthens maximum likelihood structural refinement. Acta Crystallogr 1997;D54:1285-1294.
-
(1997)
Acta Crystallogr
, vol.D54
, pp. 1285-1294
-
-
Pannu, N.S.1
Murshudov, G.N.2
Dodson, E.J.3
Read, R.4
-
16
-
-
0000574657
-
Structure of the pig insulin dimer in the cubic crystal
-
Badger J, Harris MR, Reynolds CD, Evans AC, Dodson EJ, Dodson GG, North ACT. Structure of the pig insulin dimer in the cubic crystal. Acta Crystallogr 1991;B47:127-136.
-
(1991)
Acta Crystallogr
, vol.B47
, pp. 127-136
-
-
Badger, J.1
Harris, M.R.2
Reynolds, C.D.3
Evans, A.C.4
Dodson, E.J.5
Dodson, G.G.6
North, A.C.T.7
-
17
-
-
79952608525
-
Accurate bond and angle parameters for x-ray protein structure refinement
-
Engh RA, Huber R. Accurate bond and angle parameters for x-ray protein structure refinement. Acta Crystallogr 1991;A47:392-400.
-
(1991)
Acta Crystallogr
, vol.A47
, pp. 392-400
-
-
Engh, R.A.1
Huber, R.2
-
18
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren NF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, N.F.3
DiNola, A.4
Haak, J.R.5
-
19
-
-
36749107785
-
Molecular dynamics simulations at constant pressure and/or temperature
-
Andersen HC. Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys 1980;72:2384-2393.
-
(1980)
J Chem Phys
, vol.72
, pp. 2384-2393
-
-
Andersen, H.C.1
-
20
-
-
84977303841
-
The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors
-
Marquart M, Walter J, Deisenhofer J, Bode W, Huber R. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallogr 1983;B39:480-.
-
(1983)
Acta Crystallogr
, vol.B39
, pp. 480
-
-
Marquart, M.1
Walter, J.2
Deisenhofer, J.3
Bode, W.4
Huber, R.5
-
21
-
-
0031569354
-
A mechanism for toxin insertion into membranes is suggested by the crystal structure of the channel-forming domain of colicin E1
-
Elkins P, Bunker A, Cramer WA, Stauffacher CV. A mechanism for toxin insertion into membranes is suggested by the crystal structure of the channel-forming domain of colicin E1. Structure 1997;5:443-458.
-
(1997)
Structure
, vol.5
, pp. 443-458
-
-
Elkins, P.1
Bunker, A.2
Cramer, W.A.3
Stauffacher, C.V.4
-
22
-
-
0000980729
-
Representation of phase probability distributions for simplified combination of independent phase information
-
Hendrickson WA, Lattman EE. Representation of phase probability distributions for simplified combination of independent phase information. Acta Crystallogr 1970;B26:136-143.
-
(1970)
Acta Crystallogr
, vol.B26
, pp. 136-143
-
-
Hendrickson, W.A.1
Lattman, E.E.2
-
23
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
Guntert P, Mumenthaler C, Wuthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997;273:283-298.
-
(1997)
J Mol Biol
, vol.273
, pp. 283-298
-
-
Guntert, P.1
Mumenthaler, C.2
Wuthrich, K.3
-
24
-
-
0030954481
-
Refined structure of villin 14T and a detailed comparison with other actin-severing domains
-
Markus MA, Matsudaira P, Wagner G. Refined structure of villin 14T and a detailed comparison with other actin-severing domains. Protein Sci 1997;6:1197-1209.
-
(1997)
Protein Sci
, vol.6
, pp. 1197-1209
-
-
Markus, M.A.1
Matsudaira, P.2
Wagner, G.3
-
25
-
-
0029120954
-
Solution structure of the C-terminal domain of human tfIIβ: Similarity to cyclin A an interaction with a tata-binding protein
-
Bagby S, Kim S, Maldonado E, Tong KI, Reinberg D, Ikura A. Solution structure of the C-terminal domain of human tfIIβ: similarity to cyclin A an interaction with a tata-binding protein. Cell 1995;82:857-867.
-
(1995)
Cell
, vol.82
, pp. 857-867
-
-
Bagby, S.1
Kim, S.2
Maldonado, E.3
Tong, K.I.4
Reinberg, D.5
Ikura, A.6
-
26
-
-
0344527094
-
-
San Diego: Molecular Simulations Inc
-
DeCipher User Guide, San Diego: Molecular Simulations Inc, 1997.
-
(1997)
DeCipher User Guide
-
-
-
27
-
-
0011865621
-
A computationally efficient method for evaluating the gradient of 2D NOESY intensities
-
Yip PF. A computationally efficient method for evaluating the gradient of 2D NOESY intensities. J Biomol NMR 1993;3:361-365.
-
(1993)
J Biomol NMR
, vol.3
, pp. 361-365
-
-
Yip, P.F.1
-
28
-
-
0024815191
-
Determination of the complete three-dimensional structure of the trypsin inhibitor from squash seeds in aqueous solution by nuclear magnetic resonance and a combination of distance geometry and dynamical simulated annealing
-
Holak TA, Gondol D, Otlewski J, Wilusz T. Determination of the complete three-dimensional structure of the trypsin inhibitor from squash seeds in aqueous solution by nuclear magnetic resonance and a combination of distance geometry and dynamical simulated annealing. J Mol Biol 1989;210:635-648.
-
(1989)
J Mol Biol
, vol.210
, pp. 635-648
-
-
Holak, T.A.1
Gondol, D.2
Otlewski, J.3
Wilusz, T.4
-
29
-
-
0025894164
-
Relaxation matrix refinement of the solution structure of squash trypsin inhibitor
-
Nilges M, Habazettl J, Brünger AT, Holak TA. Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. J Mol Biol 1991;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
-
-
0030750936
-
Modeling and refinement of water molecules and disordered solvent
-
Badger J. Modeling and refinement of water molecules and disordered solvent. Methods Enzymol 1997;277B:344-352.
-
(1997)
Methods Enzymol
, vol.277 B
, pp. 344-352
-
-
Badger, J.1
-
31
-
-
0030757720
-
TNT refinement package
-
Tronrud DE. TNT refinement package. Methods Enzymol 1997; 277B:306-318.
-
(1997)
Methods Enzymol
, vol.277 B
, pp. 306-318
-
-
Tronrud, D.E.1
-
33
-
-
33846446220
-
Restart procedures for the conjugate gradient method
-
Powell MJD. Restart procedures for the conjugate gradient method. Math Program 1977;12:241-254.
-
(1977)
Math Program
, vol.12
, pp. 241-254
-
-
Powell, M.J.D.1
-
34
-
-
84945074880
-
Conjugate-direction minimization: An improved method for the refinement of macromolecule
-
Tronrud DE. Conjugate-direction minimization: an improved method for the refinement of macromolecule. Acta Crystallogr 1992;A48:912-916.
-
(1992)
Acta Crystallogr
, vol.A48
, pp. 912-916
-
-
Tronrud, D.E.1
-
35
-
-
0344095835
-
-
San Diego, CA: Molecular Simulations Inc.
-
NMRchitect User Guide. San Diego, CA: Molecular Simulations Inc., 1997.
-
(1997)
NMRchitect User Guide
-
-
|