Crossref
journal-article
Elsevier BV
Journal of Structural Biology (78)
References
53
Referenced
207
10.1016/S1359-0278(97)00024-2
/ Fold. Des. / Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential by Bahar (1997)10.1073/pnas.80.21.6571
/ Proc. Natl. Acad. Sci. USA / Harmonic dynamics of proteins: normal mode and fluctuations in bovine pancreatic trypsin inhibitor by Brooks (1983)10.1073/pnas.82.15.4995
/ Proc. Natl. Acad. Sci. USA / Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme by Brooks (1985){'key': '10.1016/j.jsb.2004.03.002_BIB4', 'volume': 'vol. 71', 'author': 'Brooks III', 'year': '1988'}
by Brooks III (1988){'key': '10.1016/j.jsb.2004.03.002_BIB5', 'series-title': 'X-Plor Version 3.1. A System for X-ray Crystallography and NMR', 'author': 'Brunger', 'year': '1992'}
/ X-Plor Version 3.1. A System for X-ray Crystallography and NMR by Brunger (1992)10.1016/S0092-8674(01)00286-0
/ Cell / Structural mechanism for rifampicin inhibition of bacterial RNA polymerase by Campbell (2001)10.1006/jmbi.2002.5438
/ J. Mol. Biol. / Multi-resolution contour-based fitting of macromolecular structures by Chacon (2002)10.1016/S0022-2836(02)01426-2
/ J. Mol. Biol. / Mega-Dalton biomolecular motion captured from electron microscopy reconstructions by Chacon (2003)10.1107/S0108767394007130
/ Acta Crystallogr. A / Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function by Chapman (1995)10.1073/pnas.052054099
/ Proc. Natl. Acad. Sci. USA / Conformational flexibility of bacterial RNA polymerase by Darst (2002)10.1016/S0022-2836(02)00562-4
/ J. Mol. Biol. / Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model by Delarue (2002)10.1002/jcc.1160
/ J. Comput. Chem. / Dynamics of large proteins through hierarchical levels of coarse-grained structures by Doruker (2002)10.1002/bip.360340608
/ Biopolymers / New approach for determining low-frequency normal-modes in macromolecules by Durand (1994)10.1038/35018597
/ Nature / A ratchet-like inter-subunit reorganization of the ribosome during translocation by Frank (2000)10.1016/S0092-8674(03)00427-6
/ Cell / Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement by Gao (2003)10.1002/prot.340080308
/ Proteins / Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion by Gibrat (1990)10.1073/pnas.80.12.3696
/ Proc. Natl. Acad. Sci. USA / Dynamics of a small globular proteins in terms of low-frequency vibrational modes by Go (1983)10.1002/bip.360231216
/ Biopolymers / Variational calculation of the normal modes of a large macromolecule: methods and some initial results by Harrison (1984)10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8
/ Proteins / Analysis of domain motions by approximate normal mode calculations by Hinsen (1998)10.1016/0263-7855(96)00018-5
/ J. Mol. Graph. / VMD: visual molecular dynamics by Humphrey (1996)10.1006/jmbi.2001.4633
/ J. Mol. Biol. / Bridging the information gap: computational tools for intermediate resolution structure interpretation by Jiang (2001)10.1073/pnas.87.10.3718
/ Proc. Natl. Acad. Sci. USA / Refinement of protein dynamic structure—normal mode refinement by Kidera (1990)10.1006/jmbi.2000.4168
/ J. Mol. Biol. / Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site by Laurberg (2000){'key': '10.1016/j.jsb.2004.03.002_BIB24', 'series-title': "ARPACK User's Guide", 'author': 'Lehoucq', 'year': '1998'}
/ ARPACK User's Guide by Lehoucq (1998)10.1016/S1047-8477(03)00028-5
/ J. Struct. Biol. / Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data by Liu (2003)10.1073/pnas.082148899
/ Proc. Natl. Acad. Sci. USA / How to describe protein motion without amino acid sequence and atomic coordinates by Ming (2002)10.1073/pnas.112222299
/ Proc. Natl. Acad. Sci. USA / Domain movements in human fatty acid synthase by quantized elastic deformational model by Ming (2002)10.1073/pnas.2135471100
/ Proc. Natl. Acad. Sci. USA / Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins by Miyashita (2003)10.1006/jmbi.1996.0257
/ J. Mol. Biol. / Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures by Mouawad (1996)10.1016/0097-8485(95)00011-G
/ Comput. Chem. / Computation of low-frequency normal-modes in macromolecules—improvements to the method of diagonalization in a mixed basis and application to hemoglobin by Perahia (1995)10.1038/nature01224
/ Nature / A cryo-electron microscopic study of ribosome-bound termination factor RF2 by Rawat (2003)10.1128/JVI.75.24.11943-11947.2001
/ J. Virol. / Virus particle explorer (VIPER), a website for virus capsid structures and their computational analyses by Reddy (2001)10.1107/S0907444900009562
/ Acta Crystallogr. D / Fitting atomic models into electron-microscopy maps by Rossmann (2000)10.1006/jsbi.2002.4435
/ J. Struct. Biol. / Combining electron microscopic with X-ray crystallographic structures by Rossmann (2001)10.1038/78923
/ Nat. Struct. Biol. / Conformational changes studied by cryo-electron microscopy by Saibil (2000)10.1016/S0022-2836(05)80063-4
/ J. Mol. Biol. / Deoxymyoglobin studied by the conformational normal mode analysis 1. Dynamics of globin and the heme–globin interaction by Seno (1990)10.1016/S0969-2126(01)00135-6
/ Structure / Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryoelectron microscopy by Speir (1995)10.1016/S0022-2836(02)00135-3
/ J. Mol. Biol. / The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus by Tama (2002)10.1093/protein/14.1.1
/ Protein Eng. / Conformational change of proteins arising from normal mode calculations by Tama (2001)10.1016/j.jmb.2004.01.048
/ J. Mol. Biol. / Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis by Tama (2004)10.1016/S0022-2836(02)00627-7
/ J. Mol. Biol. / Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory by Tama (2002)10.1002/1097-0134(20001001)41:1<1::AID-PROT10>3.0.CO;2-P
/ Proteins—Structure Function and Genetics / Building-block approach for determining low-frequency normal modes of macromolecules by Tama (2000)10.1073/pnas.1632476100
/ Proc. Natl. Acad. Sci. USA / Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy by Tama (2003)- Tama, F., Feig, M., Liu, J., Brooks III, C.L., Taylor, K.A., 2004a. Myosin II ATPase inhibition requires mechanical coupling between head and S2 domains. (submitted)
10.1103/PhysRevLett.77.1905
/ Phys. Rev. Lett. / Large amplitude elastic motions in proteins from a single-parameter, atomic analysis by Tirion (1996)10.1016/S0092-8674(03)00476-8
/ Cell / Locking and unlocking of ribosomal motions by Valle (2003)10.1006/jsbi.1998.4074
/ J. Struct. Biol. / Quantitative fitting of atomic models into observed densities derived by electron microscopy by Volkmann (1999)10.1038/82008
/ Nat. Struct. Biol. / Evidence for cleft closure in actomyosin upon ADP release by Volkmann (2000)10.1073/pnas.071051098
/ Proc. Natl. Acad. Sci. USA / Three-dimensional image reconstruction of dephosphorylated smooth muscle heavy meromyosin reveals asymmetry in the interaction between myosin heads and placement of subfragment 2 by Wendt (2001)10.1006/jsbi.2000.4350
/ J. Struct. Biol. / Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data by Wriggers (2001)10.1006/jsbi.1998.4080
/ J. Struct. Biol. / Situs: a package for docking crystal structures into low-resolution maps from electron microscopy by Wriggers (1999)10.1016/S1047-8477(02)00570-1
/ J. Struct. Biol. / A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy by Wu (2003)10.1016/S0092-8674(00)81515-9
/ Cell / Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 angstrom resolution by Zhang (1999)
Dates
Type | When |
---|---|
Created | 21 years, 4 months ago (April 3, 2004, 5:19 a.m.) |
Deposited | 1 year, 3 months ago (May 8, 2024, 11:38 p.m.) |
Indexed | 2 months ago (June 19, 2025, 2:04 a.m.) |
Issued | 20 years, 11 months ago (Sept. 1, 2004) |
Published | 20 years, 11 months ago (Sept. 1, 2004) |
Published Print | 20 years, 11 months ago (Sept. 1, 2004) |
@article{Tama_2004, title={Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM}, volume={147}, ISSN={1047-8477}, url={http://dx.doi.org/10.1016/j.jsb.2004.03.002}, DOI={10.1016/j.jsb.2004.03.002}, number={3}, journal={Journal of Structural Biology}, publisher={Elsevier BV}, author={Tama, Florence and Miyashita, Osamu and Brooks III, Charles L.}, year={2004}, month=sep, pages={315–326} }