-
1
-
-
0032530836
-
A database of macromolecular motions
-
10.1093/nar/26.18.4280, 147832, 9722650
-
Gerstein M, Krebs W. A database of macromolecular motions. Nucleic Acids Res 1998, 26:4280-4290. 10.1093/nar/26.18.4280, 147832, 9722650.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.2
-
2
-
-
1042275603
-
Exploring the range of protein flexibility, from a structural proteomics perspective
-
10.1016/j.cbpa.2003.12.006, 15036151
-
Gerstein M, Echols N. Exploring the range of protein flexibility, from a structural proteomics perspective. Curr Opin Chem Biol 2004, 8:14-19. 10.1016/j.cbpa.2003.12.006, 15036151.
-
(2004)
Curr Opin Chem Biol
, vol.8
, pp. 14-19
-
-
Gerstein, M.1
Echols, N.2
-
3
-
-
20344370764
-
Allosteric mechanisms of signal transduction
-
10.1126/science.1108595, 15933191
-
Changeux JP, Edelstein SJ. Allosteric mechanisms of signal transduction. Science 2005, 308:1424-1428. 10.1126/science.1108595, 15933191.
-
(2005)
Science
, vol.308
, pp. 1424-1428
-
-
Changeux, J.P.1
Edelstein, S.J.2
-
4
-
-
48249141040
-
Allostery and cooperativity revisited
-
10.1110/ps.03259908, 2492820, 18560010
-
Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Sci 2008, 17:1295-1307. 10.1110/ps.03259908, 2492820, 18560010.
-
(2008)
Protein Sci
, vol.17
, pp. 1295-1307
-
-
Cui, Q.1
Karplus, M.2
-
5
-
-
0032584781
-
Recommendations for the presentation of NMR structures of proteins and nucleic acids
-
10.1006/jmbi.1998.1852, 9671561
-
Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, Wüthrich K. Recommendations for the presentation of NMR structures of proteins and nucleic acids. J Mol Biol 1998, 280(5):933-952. 10.1006/jmbi.1998.1852, 9671561.
-
(1998)
J Mol Biol
, vol.280
, Issue.5
, pp. 933-952
-
-
Markley, J.L.1
Bax, A.2
Arata, Y.3
Hilbers, C.W.4
Kaptein, R.5
Sykes, B.D.6
Wright, P.E.7
Wüthrich, K.8
-
6
-
-
0033505579
-
Rotational superposition: a review of methods
-
Flower DR. Rotational superposition: a review of methods. J Mol Graph Model 1999, 17:238-244.
-
(1999)
J Mol Graph Model
, vol.17
, pp. 238-244
-
-
Flower, D.R.1
-
7
-
-
9244238239
-
A mathematical model-building procedure for proteins
-
Diamond R. A mathematical model-building procedure for proteins. Acta Crystallographica 1966, 21(2):253-266.
-
(1966)
Acta Crystallographica
, vol.21
, Issue.2
, pp. 253-266
-
-
Diamond, R.1
-
8
-
-
0000408083
-
A mathematical procedure for superimposing atomic coordinates of proteins
-
McLachlan AD. A mathematical procedure for superimposing atomic coordinates of proteins. Acta Crystallographica Section A 1972, 28(6):656-657.
-
(1972)
Acta Crystallographica Section A
, vol.28
, Issue.6
, pp. 656-657
-
-
McLachlan, A.D.1
-
9
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst 1976, A32:922-923.
-
(1976)
Acta Cryst
, vol.A
, Issue.32
, pp. 922-923
-
-
Kabsch, W.1
-
10
-
-
0002404088
-
On the orthogonal transformation used for structural comparisons
-
Kearsley SK. On the orthogonal transformation used for structural comparisons. Acta Crystallographica Section A 1989, 45(2):208-210.
-
(1989)
Acta Crystallographica Section A
, vol.45
, Issue.2
, pp. 208-210
-
-
Kearsley, S.K.1
-
11
-
-
84888276663
-
Fast determination of the optimal rotational matrix for macromolecular superpositions
-
Liu P, Agrafiotis DK, Theobald DL. Fast determination of the optimal rotational matrix for macromolecular superpositions. J Comput Chem 2009,
-
(2009)
J Comput Chem
-
-
Liu, P.1
Agrafiotis, D.K.2
Theobald, D.L.3
-
12
-
-
36149010019
-
Some Studies Concerning Rotating Axes and Polyatomic Molecules
-
Eckart C. Some Studies Concerning Rotating Axes and Polyatomic Molecules. Phys Rev 1935, 47(7):552-558.
-
(1935)
Phys Rev
, vol.47
, Issue.7
, pp. 552-558
-
-
Eckart, C.1
-
13
-
-
20544436144
-
Eckart axis conditions and the minimization of the root-mean-square deviation: two closely related problems
-
10.1063/1.1929739, 15974649
-
Kudin KN, Dymarsky AY. Eckart axis conditions and the minimization of the root-mean-square deviation: two closely related problems. J Chem Phys 2005, 122:224105. 10.1063/1.1929739, 15974649.
-
(2005)
J Chem Phys
, vol.122
, pp. 224105
-
-
Kudin, K.N.1
Dymarsky, A.Y.2
-
14
-
-
44349129711
-
Eckart axis conditions, Gauss' principle of least constraint, and the optimal superposition of molecular structures
-
10.1063/1.2902290, 18500850
-
Kneller GR. Eckart axis conditions, Gauss' principle of least constraint, and the optimal superposition of molecular structures. J Chem Phys 2008, 128:194101. 10.1063/1.2902290, 18500850.
-
(2008)
J Chem Phys
, vol.128
, pp. 194101
-
-
Kneller, G.R.1
-
15
-
-
0029644168
-
Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
-
10.1016/S0969-2126(96)00018-4, 8805521
-
Müller CW, Schlauderer GJ, Reinstein J, Schulz GE. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure 1996, 4:147-156. 10.1016/S0969-2126(96)00018-4, 8805521.
-
(1996)
Structure
, vol.4
, pp. 147-156
-
-
Müller, C.W.1
Schlauderer, G.J.2
Reinstein, J.3
Schulz, G.E.4
-
16
-
-
0032533403
-
Extraction of geometrically similar substructures: least-squares and Chebyshev fitting and the difference distance matrix
-
10.1002/(SICI)1097-0134(19981115)33:3<320::AID-PROT2>3.0.CO;2-Q, 9829692
-
Lesk AM. Extraction of geometrically similar substructures: least-squares and Chebyshev fitting and the difference distance matrix. Proteins 1998, 33:320-328. 10.1002/(SICI)1097-0134(19981115)33:3<320::AID-PROT2>3.0.CO;2-Q, 9829692.
-
(1998)
Proteins
, vol.33
, pp. 320-328
-
-
Lesk, A.M.1
-
17
-
-
60649092330
-
Using least median of squares for structural superposition of flexible proteins
-
10.1186/1471-2105-10-29, 2639377, 19159484
-
Liu YS, Fang Y, Ramani K. Using least median of squares for structural superposition of flexible proteins. BMC Bioinformatics 2009, 10:29. 10.1186/1471-2105-10-29, 2639377, 19159484.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 29
-
-
Liu, Y.S.1
Fang, Y.2
Ramani, K.3
-
18
-
-
3042581007
-
Flexible structure alignment by chaining aligned fragment pairs allowing twists
-
Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003, 19(Suppl 2):i246-255.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Ye, Y.1
Godzik, A.2
-
19
-
-
45949117843
-
A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data
-
Nilges M, Clore GM, Gronenborn AM. A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data. FEBS Lett 1987, 219:17-21.
-
(1987)
FEBS Lett
, vol.219
, pp. 17-21
-
-
Nilges, M.1
Clore, G.M.2
Gronenborn, A.M.3
-
21
-
-
0029091249
-
Average core structures and variability measures for protein families: application to the immunoglobulins
-
10.1006/jmbi.1995.0423, 7643385
-
Gerstein M, Altman RB. Average core structures and variability measures for protein families: application to the immunoglobulins. J Mol Biol 1995, 251:161-175. 10.1006/jmbi.1995.0423, 7643385.
-
(1995)
J Mol Biol
, vol.251
, pp. 161-175
-
-
Gerstein, M.1
Altman, R.B.2
-
22
-
-
0030883755
-
Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
-
10.1002/(SICI)1097-0134(199709)29:1<1::AID-PROT1>3.0.CO;2-J, 9294863
-
Wriggers W, Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 1997, 29:1-14. 10.1002/(SICI)1097-0134(199709)29:1<1::AID-PROT1>3.0.CO;2-J, 9294863.
-
(1997)
Proteins
, vol.29
, pp. 1-14
-
-
Wriggers, W.1
Schulten, K.2
-
23
-
-
18844415920
-
Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
-
Snyder DA, Montelione GT. Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins Struct Funct Bioinf 2005, 59(4):673-686.
-
(2005)
Proteins Struct Funct Bioinf
, vol.59
, Issue.4
, pp. 673-686
-
-
Snyder, D.A.1
Montelione, G.T.2
-
24
-
-
33744807436
-
Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures
-
10.1529/biophysj.105.066654, 1471868, 16565070
-
Damm KL, Carlson HA. Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. Biophys J 2006, 90(12):4558-4573. 10.1529/biophysj.105.066654, 1471868, 16565070.
-
(2006)
Biophys J
, vol.90
, Issue.12
, pp. 4558-4573
-
-
Damm, K.L.1
Carlson, H.A.2
-
25
-
-
84888279153
-
Superimposition of protein structures with dynamically weighted RMSD
-
Wu D, Wu Z. Superimposition of protein structures with dynamically weighted RMSD. J Mol Model 2009,
-
(2009)
J Mol Model
-
-
Wu, D.1
Wu, Z.2
-
26
-
-
0001962564
-
The molecular modeling toolkit: A new approach to molecular simulations
-
Hinsen K. The molecular modeling toolkit: A new approach to molecular simulations. J Comp Chem 2000, 9:79-85.
-
(2000)
J Comp Chem
, vol.9
, pp. 79-85
-
-
Hinsen, K.1
-
28
-
-
0003071947
-
Scale mixtures of normal distributions
-
Andrews D, Mallows C. Scale mixtures of normal distributions. J Royal Stat Soc 1974, 36:99-102.
-
(1974)
J Royal Stat Soc
, vol.36
, pp. 99-102
-
-
Andrews, D.1
Mallows, C.2
-
29
-
-
0039713775
-
On scale mixtures of normal distributions
-
West M. On scale mixtures of normal distributions. Biometrika 1987, 74:646-648.
-
(1987)
Biometrika
, vol.74
, pp. 646-648
-
-
West, M.1
-
30
-
-
0017022589
-
A model for non-Rayleigh sea echo
-
Jakeman E, Pusey P, Establishment R, Malvern W. A model for non-Rayleigh sea echo. IEEE Transactions on Antennas and Propagation 1976, 24:806-814.
-
(1976)
IEEE Transactions on Antennas and Propagation
, vol.24
, pp. 806-814
-
-
Jakeman, E.1
Pusey, P.2
Establishment, R.3
Malvern, W.4
-
31
-
-
33748683496
-
Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem
-
10.1073/pnas.0508445103, 1664551, 17130458
-
Theobald DL, Wuttke DS. Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem. Proc Natl Acad Sci USA 2006, 103(49):18521-18527. 10.1073/pnas.0508445103, 1664551, 17130458.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.49
, pp. 18521-18527
-
-
Theobald, D.L.1
Wuttke, D.S.2
-
32
-
-
0028885711
-
Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution
-
10.1038/nsb1295-1083, 8846220
-
Braig K, Adams PD, Brünger AT. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution. Nat Struct Biol 1995, 2(12):1083-1094. 10.1038/nsb1295-1083, 8846220.
-
(1995)
Nat Struct Biol
, vol.2
, Issue.12
, pp. 1083-1094
-
-
Braig, K.1
Adams, P.D.2
Brünger, A.T.3
-
33
-
-
0030870719
-
The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex
-
10.1038/41944, 9285585
-
Xu Z, Horwich AL, Sigler PB. The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature 1997, 388(6644):741-750. 10.1038/41944, 9285585.
-
(1997)
Nature
, vol.388
, Issue.6644
, pp. 741-750
-
-
Xu, Z.1
Horwich, A.L.2
Sigler, P.B.3
-
34
-
-
17444405610
-
Structural basis of pore formation by the bacterial toxin pneumolysin
-
10.1016/j.cell.2005.02.033, 15851031
-
Tilley SJ, Orlova EV, Gilbert RJC, Andrew PW, Saibil HR. Structural basis of pore formation by the bacterial toxin pneumolysin. Cell 2005, 121(2):247-256. 10.1016/j.cell.2005.02.033, 15851031.
-
(2005)
Cell
, vol.121
, Issue.2
, pp. 247-256
-
-
Tilley, S.J.1
Orlova, E.V.2
Gilbert, R.J.C.3
Andrew, P.W.4
Saibil, H.R.5
-
35
-
-
0022429234
-
An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution
-
10.1016/0022-2836(85)90346-8, 2582141
-
Havel TF, Wüthrich K. An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J Mol Biol 1985, 182:281-294. 10.1016/0022-2836(85)90346-8, 2582141.
-
(1985)
J Mol Biol
, vol.182
, pp. 281-294
-
-
Havel, T.F.1
Wüthrich, K.2
-
36
-
-
0029159794
-
Solution structure of calcium-free calmodulin
-
10.1038/nsb0995-768, 7552748
-
Kuboniwa H, Tjandra N, Grzesiek S, Ren H, Klee CB, Bax A. Solution structure of calcium-free calmodulin. Nat Struct Biol 1995, 2(9):768-776. 10.1038/nsb0995-768, 7552748.
-
(1995)
Nat Struct Biol
, vol.2
, Issue.9
, pp. 768-776
-
-
Kuboniwa, H.1
Tjandra, N.2
Grzesiek, S.3
Ren, H.4
Klee, C.B.5
Bax, A.6
-
38
-
-
0003414592
-
-
Oxford UK: Oxford University Press, 3
-
Jeffreys H. Theory of Probability 1961, Oxford UK: Oxford University Press, 3.
-
(1961)
Theory of Probability
-
-
Jeffreys, H.1
-
41
-
-
0002629270
-
Maximum likelihood from incomplete data via the EM algorithm (with discussion)
-
Dempster AP, Laird NM, Rubin DB. Maximum likelihood from incomplete data via the EM algorithm (with discussion). J R Stat Soc B 1977, 39:1-38.
-
(1977)
J R Stat Soc B
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
42
-
-
0021518209
-
Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images
-
Geman S, Geman D. Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images. IEEE Trans PAMI 1984, 6(6):721-741.
-
(1984)
IEEE Trans PAMI
, vol.6
, Issue.6
, pp. 721-741
-
-
Geman, S.1
Geman, D.2
-
44
-
-
70449521305
-
Generation of three-dimensional random rotations in fitting and matching problems
-
Habeck M. Generation of three-dimensional random rotations in fitting and matching problems. Computational Statistics 2009, 24:719-731.
-
(2009)
Computational Statistics
, vol.24
, pp. 719-731
-
-
Habeck, M.1
-
45
-
-
0000324169
-
Adaptive Rejection Sampling for Gibbs Sampling
-
Gilks WR, Wild P. Adaptive Rejection Sampling for Gibbs Sampling. Applied Statistics 1992, 41(2):337-348.
-
(1992)
Applied Statistics
, vol.41
, Issue.2
, pp. 337-348
-
-
Gilks, W.R.1
Wild, P.2
|