-
1
-
-
0022419152
-
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
-
Levitt, M., C. Sander, and P. S. Stern. 1985. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181:423-447.
-
(1985)
J. Mol. Biol.
, vol.181
, pp. 423-447
-
-
Levitt, M.1
Sander, C.2
Stern, P.S.3
-
3
-
-
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
-
4
-
-
0033117937
-
Investigating protein dynamics in collective coordinate space
-
Kitao, A., and N. Go. 1999. Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol. 9:164-169.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 164-169
-
-
Kitao, A.1
Go, N.2
-
5
-
-
0034127361
-
Collective protein dynamics in relation to function
-
Berendsen, H. J. C., and S. Hayward. 2000. Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol. 10:165-169.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 165-169
-
-
Berendsen, H.J.C.1
Hayward, S.2
-
6
-
-
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 analysis. Protein Eng. 14:1-6. (Pubitemid 32318932)
-
(2001)
Protein Engineering
, vol.14
, Issue.1
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.-H.2
-
7
-
-
68149141470
-
Protein elastic network models and the range of cooperativity
-
In press. 10.1073/pnas.0902159106
-
Yang, L., G. Song, and R. L. Jernigan. 2009. Protein elastic network models and the range of cooperativity. Proc. Natl. Acad. Sci. USA. In press. 10.1073/pnas.0902159106.
-
(2009)
Proc. Natl. Acad. Sci. USA
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
8
-
-
0034691576
-
A ratchet-like inter-subunit reorganization of the ribosome during translocation
-
DOI 10.1038/35018597
-
Frank, J., and R. K. Agrawal. 2000. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 406:318-322. (Pubitemid 30604411)
-
(2000)
Nature
, vol.406
, Issue.6793
, pp. 318-322
-
-
Frank, J.1
Agrawal, R.K.2
-
9
-
-
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
-
10
-
-
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, et al. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515. (Pubitemid 32108200)
-
(2001)
Biophysical Journal
, vol.80
, Issue.1
, 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
-
11
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
Bahar, I., and A. J. Rader. 2005. Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol. 15:586-592.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 586-592
-
-
Bahar, I.1
Rader, A.J.2
-
12
-
-
14844286108
-
Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
-
DOI 10.1016/j.str.2005.02.002
-
Ma, J. 2005. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure. 13:373-380. (Pubitemid 40342876)
-
(2005)
Structure
, vol.13
, Issue.3
, pp. 373-380
-
-
Ma, J.1
-
13
-
-
79953103868
-
Elastic network models of coarse-grained proteins are effective for studying the structural control exerted over their dynamics
-
G. Voth, editor. CRC Press, Taylor and Francis Group, Boca Raton, FL
-
Jernigan, R. L., L. Yang, G. Song, O. Kurkcuoglu, and P. Doruker. 2008. Elastic network models of coarse-grained proteins are effective for studying the structural control exerted over their dynamics. In Coarse-Graining of Condensed Phase and Biomolecular Systems G. Voth, editor. CRC Press, Taylor and Francis Group, Boca Raton, FL. 237-254.
-
(2008)
Coarse-Graining of Condensed Phase and Biomolecular Systems
, pp. 237-254
-
-
Jernigan, R.L.1
Yang, L.2
Song, G.3
Kurkcuoglu, O.4
Doruker, P.5
-
14
-
-
0037079578
-
Dynamics of large proteins through hierarchical levels of coarse-grained structures
-
Doruker, P., R. L. Jernigan, and I. Bahar. 2002. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:119-127.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 119-127
-
-
Doruker, P.1
Jernigan, R.L.2
Bahar, I.3
-
15
-
-
0347753596
-
Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions
-
DOI 10.1016/j.polymer.2003.10.071
-
Kurkcuoglu, O., P. Doruker, and R. L. Jernigan. 2004. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions. Polymer (Guildf.). 45:649-657. (Pubitemid 38082198)
-
(2004)
Polymer
, vol.45
, Issue.2
, pp. 649-657
-
-
Kurkcuoglu, O.1
Jernigan, R.L.2
Doruker, P.3
-
16
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
DOI 10.1002/1097-0134(20001001)41:1<1::AID-PROT10>3.0.CO;2-P
-
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. (Pubitemid 30666907)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.41
, Issue.1
, pp. 1-7
-
-
Tama, F.1
Gadea, F.X.2
Marques, O.3
Sanejouand, Y.-H.4
-
17
-
-
55749115445
-
A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography
-
Lu, M., and J. Ma. 2008. A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. Proc. Natl. Acad. Sci. USA. 105:15358-15363.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 15358-15363
-
-
Lu, M.1
Ma, J.2
-
18
-
-
20544467352
-
Collective dynamics of large proteins from mixed coarse-grained elastic network model
-
Kurkcuoglu, O., P. Doruker, and R. L. Jernigan. 2005. Collective dynamics of large proteins from mixed coarse-grained elastic network model. QSAR Comb. Sci. 24:443-448.
-
(2005)
QSAR Comb. Sci.
, vol.24
, pp. 443-448
-
-
Kurkcuoglu, O.1
Doruker, P.2
Jernigan, R.L.3
-
19
-
-
31544444687
-
Loop motions of triosephosphate isomerase observed with elastic networks
-
DOI 10.1021/bi0518085
-
Kurkcuoglu, O., P. Doruker, and R. L. Jernigan. 2006. Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry. 45:1173-1182. (Pubitemid 43167184)
-
(2006)
Biochemistry
, vol.45
, Issue.4
, pp. 1173-1182
-
-
Kurkcuoglu, O.1
Jernigan, R.L.2
Doruker, P.3
-
20
-
-
38849181675
-
Dimerization affects collective dynamics of triosephosphate isomerase
-
DOI 10.1021/bi701916b
-
Cansu, S., and P. Doruker. 2008. Dimerization affects collective dynamics of triosephosphate isomerase. Biochemistry. 47:1358-1368. (Pubitemid 351198712)
-
(2008)
Biochemistry
, vol.47
, Issue.5
, pp. 1358-1368
-
-
Cansu, S.1
Doruker, P.2
-
21
-
-
67650395601
-
A docking study using atomistic conformers generated via elastic network model for cyclosporin A/cyclophilin A complex
-
Akten, D., S. Cansu, and P. Doruker. A docking study using atomistic conformers generated via elastic network model for cyclosporin A/cyclophilin A complex. J. Biomol. Struct. Dyn. 27:13-26.
-
J. Biomol. Struct. Dyn.
, vol.27
, pp. 13-26
-
-
Akten, D.1
Cansu, S.2
Doruker, P.3
-
22
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto, C. N., J. A. Kovacs, and R. A. Abagyan. 2005. Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc. 127:9632-9640.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
23
-
-
47749099638
-
Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes
-
Isin, B., K. Schulten, E. Tajkhorshid, and I. Bahar. 2008. Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes. Biophys. J. 95:789-803.
-
(2008)
Biophys. J.
, vol.95
, pp. 789-803
-
-
Isin, B.1
Schulten, K.2
Tajkhorshid, E.3
Bahar, I.4
-
24
-
-
0037764042
-
Molecular dynamics simulations of peptides and proteins with amplified collective motions
-
Zhang, Z., Y. Shi, and H. Liu. 2003. Molecular dynamics simulations of peptides and proteins with amplified collective motions. Biophys. J. 84:3583-3593. (Pubitemid 36637858)
-
(2003)
Biophysical Journal
, vol.84
, Issue.6
, pp. 3583-3593
-
-
Zhang, Z.1
Shi, Y.2
Liu, H.3
-
25
-
-
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
-
26
-
-
0032483483
-
Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms
-
Bahar, I., and R. L. Jernigan. 1998. Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. J. Mol. Biol. 281:871-884.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 871-884
-
-
Bahar, I.1
Jernigan, R.L.2
-
27
-
-
0036077875
-
Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
-
Delarue, M., and Y. H. Sanejouand. 2002. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J. Mol. Biol. 320:1011-1024.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 1011-1024
-
-
Delarue, M.1
Sanejouand, Y.H.2
-
29
-
-
0037080323
-
Molecular mechanisms of chaperonin GroEL-GroES function
-
DOI 10.1021/bi011393x
-
Keskin, O., I. Bahar, D. Flatow, D. G. Covell, and R. L. Jernigan. 2002. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 41:491-501. (Pubitemid 34062018)
-
(2002)
Biochemistry
, vol.41
, Issue.2
, pp. 491-501
-
-
Keskin, O.1
Bahar, I.2
Flatow, D.3
Covell, D.G.4
Jernigan, R.L.5
-
30
-
-
33746545621
-
Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations
-
Doruker, P., L. Nilsson, and O. Kurkcuoglu. 2006. Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations. J. Biomol. Struct. Dyn. 24:1-15.
-
(2006)
J. Biomol. Struct. Dyn.
, vol.24
, pp. 1-15
-
-
Doruker, P.1
Nilsson, L.2
Kurkcuoglu, O.3
-
31
-
-
33644929350
-
Multiscale coarse graining of liquid-state systems
-
Izvekov, S., and G. A. Voth. 2005. Multiscale coarse graining of liquid-state systems. J. Chem. Phys. 123:134105-134113.
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 134105-134113
-
-
Izvekov, S.1
Voth, G.A.2
-
32
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
DOI 10.1002/prot.340230410
-
Marques, O., and Y. H. Sanejouand. 1995. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins. 23:557-560. (Pubitemid 26009518)
-
(1995)
Proteins: Structure, Function and Genetics
, vol.23
, Issue.4
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.-H.2
-
33
-
-
58149305886
-
-
Boeing Computer Services, Seattle, WA
-
Grimes, R. G., J. G. Lewis, and H. D. Simon. 1991. A Shifted Block Lanczos Algorithm for Solving Sparse Symmetric Eigenvalue Problems. Boeing Computer Services, Seattle, WA.
-
(1991)
A Shifted Block Lanczos Algorithm for Solving Sparse Symmetric Eigenvalue Problems
-
-
Grimes, R.G.1
Lewis, J.G.2
Simon, H.D.3
-
34
-
-
21244466002
-
-
University of California, San Francisco
-
Case, D. A., T. A. Darden, T. E. I. Cheatham, C. L. Simmerling, J. Wang, et al. 2004. AMBER, Version 8. University of California, San Francisco.
-
(2004)
AMBER, Version 8
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.I.3
Simmerling, C.L.4
Wang, J.5
-
35
-
-
23444454552
-
The AMBER biomolecular simulation programs
-
Case, D. A., T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, et al. 2005. The AMBER biomolecular simulation programs. J. Comput. Chem. 26:1668-1688.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
-
36
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins
-
Duan, Y., C. Wu, S. Chowdhury, M. C. Lee, G. Xiong, et al. 2003. A point-charge force field for molecular mechanics simulations of proteins. J. Comput. Chem. 24:1999-2012.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
-
37
-
-
0002636134
-
Pairwise solute descreening of solute charges from a dielectric medium
-
Hawkins, G. D., C. J. Cramer, and D. G. Truhlar. 1995. Pairwise solute descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 246:122-129.
-
(1995)
Chem. Phys. Lett.
, vol.246
, pp. 122-129
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
38
-
-
33748390341
-
Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
-
Hawkins, G. D., C. J. Cramer, and D. G. Truhlar. 1996. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem. 100:19824-19839.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 19824-19839
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
39
-
-
0033468737
-
Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects
-
Srinivasan, J., M. W. Trevathan, P. Beroza, and D. A. Case. 1999. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects. Theor. Chem. Acc. 101:426-434.
-
(1999)
Theor. Chem. Acc.
, vol.101
, pp. 426-434
-
-
Srinivasan, J.1
Trevathan, M.W.2
Beroza, P.3
Case, D.A.4
-
40
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, et al. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
41
-
-
0028209049
-
Crystal structure of recombinant chicken triosephosphate isomerase- Phosphoglycolohydroxamate complex at 1.8-Å resolution
-
Zhang, Z., S. Sugio, E. A. Komives, K. D. Liu, J. R. Knowles, et al. 1994. Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8 Å resolution. Biochemistry. 33:2830-2837. (Pubitemid 24103341)
-
(1994)
Biochemistry
, vol.33
, Issue.10
, pp. 2830-2837
-
-
Zhang, Z.1
Sugio, S.2
Komives, E.A.3
Liu, K.D.4
Knowles, J.R.5
Petsko, G.A.6
Ringe, D.7
-
42
-
-
0025763437
-
Enzyme catalysis: Not different, just better
-
Knowles, J. R. 1991. Enzyme catalysis: not different, just better. Nature. 350:121-124.
-
(1991)
Nature
, vol.350
, pp. 121-124
-
-
Knowles, J.R.1
-
43
-
-
0345894320
-
Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation
-
DOI 10.1021/bi026994i
-
Desamero, R., S. Rozovsky, N. Zhadin, A. McDermott, and R. Callender. 2003. Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation. Biochemistry. 42:2941-2951. (Pubitemid 36331538)
-
(2003)
Biochemistry
, vol.42
, Issue.10
, pp. 2941-2951
-
-
Desamero, R.1
Rozovsky, S.2
Zhadin, N.3
McDermott, A.4
Callender, R.5
-
44
-
-
4444321214
-
Entropy effects on protein hinges: The reaction catalyzed by triosephosphate isomerase
-
DOI 10.1021/bi049208d
-
Xiang, J., J. Jung, and N. S. Sampson. 2004. Entropy effects on protein hinges: the reaction catalyzed by triosephosphate isomerase. Biochemistry. 43:11436-11445. (Pubitemid 39186965)
-
(2004)
Biochemistry
, vol.43
, Issue.36
, pp. 11436-11445
-
-
Xiang, J.1
Jung, J.-Y.2
Sampson, N.S.3
-
45
-
-
1442277682
-
Computational modeling of the catalytic reaction in triose phosphate isomerase
-
Guallar, V., M. Jacobson, A. McDermott, and R. A. Friesner. 2004. Computational modeling of the catalytic reaction in triose phosphate isomerase. J. Mol. Biol. 337:227-239.
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 227-239
-
-
Guallar, V.1
Jacobson, M.2
McDermott, A.3
Friesner, R.A.4
-
46
-
-
0015819192
-
Refolding of triose phosphate isomerase
-
Waley, S. G. 1973. Refolding of triose phosphate isomerase. Biochem. J. 135:165-172.
-
(1973)
Biochem. J.
, vol.135
, pp. 165-172
-
-
Waley, S.G.1
-
47
-
-
0019089331
-
Folding and association of triosephosphate isomerase from rabbit muscle
-
Zabori, S., R. Rudolph, and R. Jaenicke. 1980. Folding and association of triosephosphate isomerase from rabbit muscle. Z. Naturforsch. C. 35C:999-1004.
-
(1980)
Z. Naturforsch. C
, vol.35 C
, pp. 999-1004
-
-
Zabori, S.1
Rudolph, R.2
Jaenicke, R.3
-
48
-
-
0026779802
-
Segmental movement: Definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase
-
Sampson, N. S., and J. R. Knowles. 1992. Segmental movement: definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase. Biochemistry. 31:8482-8487.
-
(1992)
Biochemistry
, vol.31
, pp. 8482-8487
-
-
Sampson, N.S.1
Knowles, J.R.2
-
49
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
-
DOI 10.1126/science.289.5481.905
-
Ban, N., P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 289:905-920. (Pubitemid 30659939)
-
(2000)
Science
, vol.289
, Issue.5481
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
50
-
-
0033543589
-
Recognition of the codon-anticodon helix by ribosomal RNA
-
DOI 10.1126/science.285.5434.1722
-
Yoshizawa, S., D. Fourmy, and J. D. Puglisi. 1999. Recognition of the codon-anticodon helix by ribosomal RNA. Science. 285:1722-1725. (Pubitemid 29428870)
-
(1999)
Science
, vol.285
, Issue.5434
, pp. 1722-1725
-
-
Yoshizawa, S.1
Fourmy, D.2
Puglisi, J.D.3
-
51
-
-
33751103912
-
Structural basis for messenger RNA movement on the ribosome
-
DOI 10.1038/nature05281, PII NATURE05281
-
Yusupova, G., L. Jenner, B. Rees, D. Moras, and M. Yusupov. 2006. Structural basis for messenger RNA movement on the ribosome. Nature. 444:391-394. (Pubitemid 44764117)
-
(2006)
Nature
, vol.444
, Issue.7117
, pp. 391-394
-
-
Yusupova, G.1
Jenner, L.2
Rees, B.3
Moras, D.4
Yusupov, M.5
-
52
-
-
0034677211
-
Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12
-
Wahl, M. C., G. P. Bourenkov, H. D. Bartunik, and R. Huber. 2000. Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12. EMBO J. 19:174-186.
-
(2000)
EMBO J.
, vol.19
, pp. 174-186
-
-
Wahl, M.C.1
Bourenkov, G.P.2
Bartunik, H.D.3
Huber, R.4
-
53
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama, F., M. Valle, J. Frank, and C. L. Brooks, III. 2003. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. USA. 100:9319-9323.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks III, C.L.4
-
54
-
-
24144478280
-
Exploring global motions and correlations in the ribosome
-
DOI 10.1529/biophysj.104.058495
-
Trylska, J., V. Tozzini, and J. A. McCammon. 2005. Exploring global motions and correlations in the ribosome. Biophys. J. 89:1455-1463. (Pubitemid 41233505)
-
(2005)
Biophysical Journal
, vol.89
, Issue.3
, pp. 1455-1463
-
-
Trylska, J.1
Tozzini, V.2
McCammon, J.A.3
-
55
-
-
34249944597
-
Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution
-
Poon, B. K., X. Chen, M. Lu, N. K. Vyas, F. A. Quiocho, et al. 2007. Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution. Proc. Natl. Acad. Sci. USA. 104:7869-7874.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 7869-7874
-
-
Poon, B.K.1
Chen, X.2
Lu, M.3
Vyas, N.K.4
Quiocho, F.A.5
-
56
-
-
0032802062
-
On the convergence of the conformational coordinates basis set obtained by the Essential Dynamics analysis of proteins' molecular dynamics simulations
-
DOI 10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U
-
Amadei, A., M. A. Ceruso, and A. D. Nola. 1999. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins. 36:419-424. (Pubitemid 29387740)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.36
, Issue.4
, pp. 419-424
-
-
Amadei, A.1
Ceruso, M.A.2
Di Nola, A.3
-
57
-
-
25844525600
-
The role of shape in determining molecular motions
-
Lu, M., and J. Ma. 2005. The role of shape in determining molecular motions. Biophys. J. 89:2395-2401.
-
(2005)
Biophys. J.
, vol.89
, pp. 2395-2401
-
-
Lu, M.1
Ma, J.2
-
58
-
-
0029000872
-
Dynamics of the flexible loop triosephosphate isomerase; the loop motion is not ligand gated
-
Williams, J. C., and A. E. McDermott. 1995. Dynamics of the flexible loop triosephosphate isomerase; The loop motion is not ligand gated. Biochemistry. 34:8309-8319.
-
(1995)
Biochemistry
, vol.34
, pp. 8309-8319
-
-
Williams, J.C.1
McDermott, A.E.2
-
59
-
-
0037441653
-
Structure validation by C-alpha geometry: Phi, psi and C-beta deviation
-
Lovell, S. C., I. W. Davis, W. B. Arendall, III, P. I. W. de Bakker, J. M. Word, et al. 2003. Structure validation by C-alpha geometry: phi, psi and C-beta deviation. Proteins. 50:437-450.
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall III, W.B.3
De Bakker, P.I.W.4
Word, J.M.5
-
60
-
-
34547592557
-
MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
-
Davis, I. W., A. Leaver-Fay, V. B. Chen, J. N. Block, G. J. Kapral, et al. 2007. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35:W375-W383.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Davis, I.W.1
Leaver-Fay, A.2
Chen, V.B.3
Block, J.N.4
Kapral, G.J.5
-
61
-
-
0032982866
-
EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
-
Agrawal, R. K., A. B. Heagle, P. Penczek, R. A. Grassucci, and J. Frank. 1999. EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nat. Struct. Biol. 6:643-647.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 643-647
-
-
Agrawal, R.K.1
Heagle, A.B.2
Penczek, P.3
Grassucci, R.A.4
Frank, J.5
-
62
-
-
0030582394
-
Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice
-
Lata, K. R., R. K. Agrawal, P. Penczek, R. Grassucci, J. Zhu, et al. 1996. Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice. J. Mol. Biol. 262:43-52.
-
(1996)
J. Mol. Biol.
, vol.262
, pp. 43-52
-
-
Lata, K.R.1
Agrawal, R.K.2
Penczek, P.3
Grassucci, R.4
Zhu, J.5
-
63
-
-
0037184536
-
Selection of tRNA by the ribosome requires a transition from an open to a closed form
-
Ogle, J. M., F. V. Murphy, M. J. Tarry, and V. Ramakrishnan. 2002. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell. 111:721-732.
-
(2002)
Cell
, vol.111
, pp. 721-732
-
-
Ogle, J.M.1
Murphy, F.V.2
Tarry, M.J.3
Ramakrishnan, V.4
-
64
-
-
0035943352
-
Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G dependent translocation
-
Agrawal, R. K., J. Linde, J. Sengupta, K. H. Nierhaus, and J. Frank. 2001. Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G dependent translocation. J. Mol. Biol. 311:777-787.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 777-787
-
-
Agrawal, R.K.1
Linde, J.2
Sengupta, J.3
Nierhaus, K.H.4
Frank, J.5
-
65
-
-
0037963475
-
Locking and unlocking of ribosomal motions
-
Valle, M., A. Zavialov, J. Sengupta, U. Rawat, M. Ehrenberg, et al. 2003. Locking and unlocking of ribosomal motions. Cell. 114:123-134.
-
(2003)
Cell
, vol.114
, pp. 123-134
-
-
Valle, M.1
Zavialov, A.2
Sengupta, J.3
Rawat, U.4
Ehrenberg, M.5
-
66
-
-
0034699519
-
Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
-
Carter, A. P., W. M. Clemons, Jr., D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly, et al. 2000. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 407:340-348.
-
(2000)
Nature
, vol.407
, pp. 340-348
-
-
Carter, A.P.1
Clemons Jr., W.M.2
Brodersen, D.E.3
Morgan-Warren, R.J.4
Wimberly, B.T.5
-
67
-
-
25144480034
-
Improving on nature: Antibiotics that target the ribosome
-
Sutcliffe, J. A. 2005. Improving on nature: antibiotics that target the ribosome. Curr. Opin. Microbiol. 8:534-542.
-
(2005)
Curr. Opin. Microbiol.
, vol.8
, pp. 534-542
-
-
Sutcliffe, J.A.1
|