-
1
-
-
33847005283
-
Correlations in the motion of atoms in liquid argon
-
Rahman, A. 1964. Correlations in the motion of atoms in liquid argon. Phys. Rev. A. 136:405-411.
-
(1964)
Phys. Rev. A
, vol.136
, pp. 405-411
-
-
Rahman, A.1
-
2
-
-
51149211502
-
Improved simulation of liquid water by molecular dynamics
-
Stillinger, F. H., and A. Rahman. 1974. Improved simulation of liquid water by molecular dynamics. J. Chem. Phys. 60:1545-1557.
-
(1974)
J. Chem. Phys
, vol.60
, pp. 1545-1557
-
-
Stillinger, F.H.1
Rahman, A.2
-
4
-
-
0032530836
-
A database of macromolecular motions
-
Gerstein, M., and W. Krebs. 1998. A database of macromolecular motions. Nucleic Acids Res. 26:4280-4290.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.2
-
5
-
-
33644873452
-
The database of macromolecular motions: New features added at the decade mark
-
Flores, S., N. Echols, D. Milburn, B. Hespenheide, K. Keating, J. Lu, S. Wells, E. Z. Yu, M. Thorpe, and M. Gerstein. 2006. The database of macromolecular motions: new features added at the decade mark. Nucleic Acids Res. 34:D296-D301.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Flores, S.1
Echols, N.2
Milburn, D.3
Hespenheide, B.4
Keating, K.5
Lu, J.6
Wells, S.7
Yu, E.Z.8
Thorpe, M.9
Gerstein, M.10
-
6
-
-
0022111715
-
Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
-
Brooks, B., and M. Karplus. 1985. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA. 82:4995-4999.
-
(1985)
Proc. Natl. Acad. Sci. USA
, vol.82
, pp. 4995-4999
-
-
Brooks, B.1
Karplus, M.2
-
7
-
-
0001031179
-
Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
-
Brooks, C. L., M. Karplus, and B. M. Pettitt. 1988. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. Adv. Chem. Phys. 71:1-249.
-
(1988)
Adv. Chem. Phys
, vol.71
, pp. 1-249
-
-
Brooks, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
8
-
-
0028331255
-
Normal mode analysis of protein dynamics
-
Case, D. A. 1994. Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4:285-290.
-
(1994)
Curr. Opin. Struct. Biol
, vol.4
, pp. 285-290
-
-
Case, D.A.1
-
9
-
-
0021701376
-
Variational calculation of the normal modes of a large macromolecule: Methods and some initial results
-
Harrison, R. W. 1984. Variational calculation of the normal modes of a large macromolecule: methods and some initial results. Biopolymers. 23:2943-2949.
-
(1984)
Biopolymers
, vol.23
, pp. 2943-2949
-
-
Harrison, R.W.1
-
10
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normalmode calculations
-
Marques, O., and Y. H. Sanejouand. 1995. Hinge-bending motion in citrate synthase arising from normalmode calculations. Proteins. 23:557-560.
-
(1995)
Proteins
, vol.23
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.H.2
-
11
-
-
0029374782
-
Computation of low-frequency normal modes in macromolecules: Improvements to the method of diagonalization in a mixed basis and application to hemoglobin
-
Perahia, D., and L. Mouawad. 1995. Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin. Comput. Chem. 19:241-246.
-
(1995)
Comput. Chem
, vol.19
, pp. 241-246
-
-
Perahia, D.1
Mouawad, L.2
-
12
-
-
0141792364
-
Allosteric changes in protein structure computed by a simple mechanical model: Hemoglobin T4R2 transition
-
Xu, C., D. Tobi, and I. Bahar. 2003. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T4R2 transition. J. Mol. Biol. 333:153-168.
-
(2003)
J. Mol. Biol
, vol.333
, pp. 153-168
-
-
Xu, C.1
Tobi, D.2
Bahar, I.3
-
13
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama, F., and Y. H. Sanejouand. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:1-6.
-
(2001)
Protein Eng
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
14
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
Krebs, W. G., V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, and M. Gerstein. 2002. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 48:682-695.
-
(2002)
Proteins
, vol.48
, pp. 682-695
-
-
Krebs, W.G.1
Alexandrov, V.2
Wilson, C.A.3
Echols, N.4
Yu, H.5
Gerstein, M.6
-
15
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
-
(1996)
Phys. Rev. Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
16
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
-
(1997)
Fold. Des
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
17
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
18
-
-
0345973041
-
Gaussian dynamics of folded proteins
-
Haliloglu, T., I. Bahar, and B. Erman. 1997. Gaussian dynamics of folded proteins. Phys. Rev. Lett. 79:3090-3093.
-
(1997)
Phys. Rev. Lett
, vol.79
, pp. 3090-3093
-
-
Haliloglu, T.1
Bahar, I.2
Erman, B.3
-
19
-
-
0000496772
-
Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability
-
Bahar, I., A. R. Atilgan, M. C. Demirel, and B. Erman. 1998. Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys. Rev. Lett. 80:2733-2736.
-
(1998)
Phys. Rev. Lett
, vol.80
, pp. 2733-2736
-
-
Bahar, I.1
Atilgan, A.R.2
Demirel, M.C.3
Erman, B.4
-
20
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan, A. R., S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
-
(2001)
Biophys. J
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
21
-
-
0032749098
-
Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with x-ray diffraction and NMR relaxation data
-
Haliloglu, T., and I. Bahar. 1999. Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with x-ray diffraction and NMR relaxation data. Proteins. 37:654-667.
-
(1999)
Proteins
, vol.37
, pp. 654-667
-
-
Haliloglu, T.1
Bahar, I.2
-
22
-
-
0035996990
-
Dynamics of proteins in crystals: Comparison of experiment with simple models
-
Kundu, S., J. S. Melton, D. C. Sorensen, and G. N. Phillips, Jr. 2002. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys. J. 83:723-732.
-
(2002)
Biophys. J
, vol.83
, pp. 723-732
-
-
Kundu, S.1
Melton, J.S.2
Sorensen, D.C.3
Phillips Jr., G.N.4
-
23
-
-
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. 23:38-48.
-
(1995)
Proteins
, vol.23
, pp. 38-48
-
-
Nichols, W.L.1
Rose, G.D.2
Eyck, L.F.T.3
Zimm, B.H.4
-
24
-
-
0030883755
-
Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
-
Wriggers, W., and K. Schulten. 1997. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins. 29:1-14.
-
(1997)
Proteins
, vol.29
, pp. 1-14
-
-
Wriggers, W.1
Schulten, K.2
-
25
-
-
0033557178
-
Analysis of domain motions in large proteins
-
Hinsen, K., A. Thomas, and M. J. Field. 1999. Analysis of domain motions in large proteins. Proteins. 34:369-382.
-
(1999)
Proteins
, vol.34
, pp. 369-382
-
-
Hinsen, K.1
Thomas, A.2
Field, M.J.3
-
26
-
-
33645019704
-
An enhanced elastic network model to represent the motions of domain-swapped proteins
-
Song, G., and R. L. Jernigan. 2006. An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins. 63:197-209.
-
(2006)
Proteins
, vol.63
, pp. 197-209
-
-
Song, G.1
Jernigan, R.L.2
-
27
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
Tama, F., F. X. Gadea, O. Marques, and Y. H. Sanejouand. 2000. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins. 41:1-7.
-
(2000)
Proteins
, vol.41
, pp. 1-7
-
-
Tama, F.1
Gadea, F.X.2
Marques, O.3
Sanejouand, Y.H.4
-
29
-
-
0025066772
-
Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion
-
Gibrat, J. F., and N. Go. 1990. Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins. 8:258-279.
-
(1990)
Proteins
, vol.8
, pp. 258-279
-
-
Gibrat, J.F.1
Go, N.2
-
30
-
-
0035427398
-
Protein flexibility predictions using graph theory
-
Jacobs, D. J., A. J. Rader, L. A. Kuhn, and M. F. Thorpe. 2001. Protein flexibility predictions using graph theory. Proteins. 44:150-165.
-
(2001)
Proteins
, vol.44
, pp. 150-165
-
-
Jacobs, D.J.1
Rader, A.J.2
Kuhn, L.A.3
Thorpe, M.F.4
-
31
-
-
10344230919
-
Automatic domain decomposition of proteins by a Gaussian network model
-
Kundu S, Sorensen D. C., and Phillips G. N. Jr. 2004. Automatic domain decomposition of proteins by a Gaussian network model. Proteins. 57:725-733.
-
(2004)
Proteins
, vol.57
, pp. 725-733
-
-
Kundu, S.1
Sorensen, D.C.2
Phillips Jr., G.N.3
-
32
-
-
0000440667
-
Residue coordination in proteins conforms to the closest packing of spheres
-
Bagci, Z., R. L. Jernigan, and I. Bahar. 2002. Residue coordination in proteins conforms to the closest packing of spheres. Polym. 43:451-459.
-
(2002)
Polym
, vol.43
, pp. 451-459
-
-
Bagci, Z.1
Jernigan, R.L.2
Bahar, I.3
-
33
-
-
0036470527
-
Residue packing in proteins: Uniform distribution on a coarse-grained scale
-
Bagci, Z., R. L. Jernigan, and I. Bahar. 2002. Residue packing in proteins: uniform distribution on a coarse-grained scale. J. Chem. Phys. 116:2269-2276.
-
(2002)
J. Chem. Phys
, vol.116
, pp. 2269-2276
-
-
Bagci, Z.1
Jernigan, R.L.2
Bahar, I.3
-
34
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
Wang, Y., A. J. Rader, I. Bahar, and R. L. Jernigan. 2004. Global ribosome motions revealed with elastic network model. J. Struct. Biol. 147:302-314.
-
(2004)
J. Struct. Biol
, vol.147
, pp. 302-314
-
-
Wang, Y.1
Rader, A.J.2
Bahar, I.3
Jernigan, R.L.4
-
35
-
-
33746102627
-
Atom-by-atom analysis of global downhill protein folding
-
Sadqi, M., D. Fushman, and V. Munõz. 2006. Atom-by-atom analysis of global downhill protein folding. Nature. 442:317-321.
-
(2006)
Nature
, vol.442
, pp. 317-321
-
-
Sadqi, M.1
Fushman, D.2
Munõz, V.3
-
36
-
-
33746325516
-
Proteins downhill all the way
-
Kelly, J. W. 2006. Proteins downhill all the way. Nature. 442:255-256.
-
(2006)
Nature
, vol.442
, pp. 255-256
-
-
Kelly, J.W.1
|