Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 487

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes

Open access
Ma, Jianpeng·2005·Structure
DOI 10.1016/j.str.2005.02.002
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.str.2005.02.002

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 1 references

Research works printed but not linked: 82

  1. Atilgan, 2001, Anisotropy of fluctuation dynamics of proteins with an elastic network model, Biophys. J., 80, 505, 10.1016/S0006-3495(01)76033-X · DOI · Paper page
  2. Bahar, 1997, Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Fold. Des., 2, 173, 10.1016/S1359-0278(97)00024-2 · DOI · Paper page
  3. Balog, 2004, Direct determination of vibrational density of states change on ligand binding to a protein, Phys. Rev. Lett., 93, 028103, 10.1103/PhysRevLett.93.028103 · doi:10.1103/physrevlett.93.028103
  4. Ban, 2000, The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution, Science, 289, 905, 10.1126/science.289.5481.905 · DOI · Paper page
  5. Beuron, 2003, Motions and negative cooperativity between p97 domains revealed by cryoelectron microscopy and quantized elastic deformational model, J. Mol. Biol., 327, 619, 10.1016/S0022-2836(03)00178-5 · DOI
  6. Braig, 1994, The crystal structure of the bacterial chaperonin GroEL at 2.8 Å, Nature, 371, 578, 10.1038/371578a0 · DOI · Paper page
  7. Brink, 2004, Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis, Structure (Camb.), 12, 185, 10.1016/j.str.2004.01.015 · DOI
  8. Brooks, 1985, Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme, Proc. Natl. Acad. Sci. USA, 82, 4995, 10.1073/pnas.82.15.4995 · DOI · Paper page
  9. Brooks, 1988, Proteins: a theoretical perspective of dynamics, structure, and thermodynamics, Adv. Chem. Phys., 71, 1
  10. Bruccoleri, 1986, The hinge-bending mode of a lysozyme-inhibitor complex, Biopolymers, 25, 1767, 10.1002/bip.360250916 · doi:10.1002/bip.360250916
  11. Carazo, 2004, Accessing information on the conformational flexibility of molecular machines, Structure, 12, 170, 10.1016/j.str.2004.01.017 · doi:10.1016/j.str.2004.01.017
  12. Chacon, 2003, Mega-dalton biomolecular motion captured from electron microscopy reconstructions, J. Mol. Biol., 326, 485, 10.1016/S0022-2836(02)01426-2 · DOI
  13. Cui, 2004, A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase, J. Mol. Biol., 340, 345, 10.1016/j.jmb.2004.04.044 · DOI
  14. Cusack, 1988, Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment, J. Mol. Biol., 202, 903, 10.1016/0022-2836(88)90566-9 · doi:10.1016/0022-2836(88)90566-9
  15. Deak, 1998, Ultrafast phase grating studies of heme proteins: observation of the low-frequency modes directing functionally important protein motions, J. Phys. Chem., 102, 6621, 10.1021/jp980492q · doi:10.1021/jp980492q
  16. Diamond, 1990, On the use of normal modes in thermal parameters refinement: theory and application to the bovine pancreatic trypsin inhibitor, Acta Crystallogr. A, 46, 425, 10.1107/S0108767390002082 · DOI
  17. Doruker, 2002, Dynamic of large proteins through hierarchical levels of coarse-grained structures, J. Comput. Chem., 23, 119, 10.1002/jcc.1160 · DOI · Paper page
  18. Emberly, 2003, Flexibility of alpha-helices: results of a statistical analysis of database protein structures, J. Mol. Biol., 327, 229, 10.1016/S0022-2836(03)00097-4 · DOI
  19. Flynn, 2004, Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament, Biophys. J., 86, 3204, 10.1016/S0006-3495(04)74368-4 · DOI
  20. Gao, 2003, A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase, Proc. Natl. Acad. Sci. USA, 100, 11339, 10.1073/pnas.1334188100 · doi:10.1073/pnas.1334188100
  21. Goh, 2004, Conformational changes associated with protein-protein interactions, Curr. Opin. Struct. Biol., 14, 104, 10.1016/j.sbi.2004.01.005 · DOI · Paper page
  22. Haliloglu, 1997, Gaussian dynamics of folded proteins, Phys. Rev. Lett., 79, 3090, 10.1103/PhysRevLett.79.3090 · DOI · Paper page
  23. Hinsen, 1998, Analysis of domain motions by approximate normal mode calculations, Proteins, 33, 417, 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8 · DOI · Paper page
  24. Hinsen, 2000, Harmonicity in slow protein dynamics, Chem. Phys., 261, 25, 10.1016/S0301-0104(00)00222-6 · DOI · Paper page
  25. Horovitz, 2000, On the relationship between the hill coefficients for steady-state and transient kinetic data: A criterion for concerted transitions in allosteric proteins, Bull. Math. Biol., 62, 241, 10.1006/bulm.1999.0150 · doi:10.1006/bulm.1999.0150
  26. Horovitz, 2001, Review: allostery in chaperonins, J. Struct. Biol., 135, 104, 10.1006/jsbi.2001.4377 · DOI
  27. Karplus, 2004, Biomolecular motors: the F1-ATPase paradigm, Curr. Opin. Struct. Biol., 14, 250, 10.1016/j.sbi.2004.03.012 · DOI
  28. Kern, 2003, The role of dynamics in allosteric regulation, Curr. Opin. Struct. Biol., 13, 748, 10.1016/j.sbi.2003.10.008 · DOI · Paper page
  29. Keskin, 2002, Molecular mechanisms of chaperonin GroEL-GroES function, Biochemistry, 41, 491, 10.1021/bi011393x · DOI
  30. Kidera, 1992, Normal mode refinement: crystallographic refinement of protein dynamic structure applied to human lysozyme, Biopolymers, 32, 315, 10.1002/bip.360320404 · DOI
  31. Kong, 2003, Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model, J. Mol. Biol., 330, 129, 10.1016/S0022-2836(03)00555-2 · DOI
  32. Kottalam, 1990, Langevin modes of macromolecules: applications to crambin and DNA hexamers, Biopolymers, 29, 1409, 10.1002/bip.360291008 · DOI
  33. Krebs, 2002, Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic, Proteins, 48, 682, 10.1002/prot.10168 · DOI · Paper page
  34. Kumar, 2000, Folding and binding cascades: dynamic landscapes and population shifts, Protein Sci., 9, 10, 10.1110/ps.9.1.10 · DOI · Paper page
  35. Kundu, 2002, Dynamics of proteins in crystals: comparison of experiment with simple models, Biophys. J., 83, 723, 10.1016/S0006-3495(02)75203-X · DOI · Paper page
  36. Lamm, 1986, Langevin modes of macromolecules, J. Chem. Phys., 85, 7334, 10.1063/1.451373 · DOI
  37. Leo-Macias, 2005, An analysis of core deformations in protein superfamilies, Biophys. J., 88, 1291, 10.1529/biophysj.104.052449 · DOI
  38. Levitt, 1985, Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme, J. Mol. Biol., 181, 423, 10.1016/0022-2836(85)90230-X · DOI · Paper page
  39. Li, 2002, A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase, Biophys. J., 83, 2457, 10.1016/S0006-3495(02)75257-0 · DOI · Paper page
  40. Lipscomb, 1983, Structure and catalysis of enzymes, Annu. Rev. Biochem., 52, 17, 10.1146/annurev.bi.52.070183.000313 · DOI
  41. Ma, 2004, New advances in normal mode analysis of supermolecular complexes and applications to structural refinement, Curr. Protein Pept. Sci., 5, 119, 10.2174/1389203043486892 · doi:10.2174/1389203043486892
  42. Ma, 1997, Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis, J. Mol. Biol., 274, 114, 10.1006/jmbi.1997.1313 · DOI
  43. Ma, 1998, The allosteric mechanism of the chaperonin GroEL: a dynamic analysis, Proc. Natl. Acad. Sci. USA, 95, 8502, 10.1073/pnas.95.15.8502 · DOI · Paper page
  44. Ma, 2000, A dynamic model for the allosteric mechanism of GroEL, J. Mol. Biol., 302, 303, 10.1006/jmbi.2000.4014 · DOI · Paper page
  45. Ma, 2002, A dynamic analysis of the rotation mechanism for conformational change in F1-ATPase, Structure, 10, 921, 10.1016/S0969-2126(02)00789-X · DOI
  46. MacKerell, 1998, All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem., B102, 3586, 10.1021/jp973084f · DOI · Paper page
  47. Ming, 2002, How to describe protein motion without amino-acid sequence and atomic coordinates, Proc. Natl. Acad. Sci. USA, 99, 8620, 10.1073/pnas.082148899 · DOI · Paper page
  48. Ming, 2002, Domain movements in human fatty acid synthase by quantized elastic deformational model, Proc. Natl. Acad. Sci. USA, 99, 7895, 10.1073/pnas.112222299 · DOI
  49. Ming, 2003, Simulation of F-actin filaments of several microns, Biophys. J., 85, 27, 10.1016/S0006-3495(03)74451-8 · doi:10.1016/s0006-3495(03)74451-8
  50. Ming, 2003, Substructure synthesis method for simulating large molecular complexes, Proc. Natl. Acad. Sci. USA, 100, 104, 10.1073/pnas.232588999 · DOI
  51. Miyashita, 2003, Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins, Proc. Natl. Acad. Sci. USA, 100, 12570, 10.1073/pnas.2135471100 · DOI · Paper page
  52. Murzin, 1995, SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol., 247, 536, 10.1016/S0022-2836(05)80134-2 · DOI
  53. Perutz, 1969, The Croonian Lecture, 1968. The haemoglobin molecule, Proc. R. Soc. Lond. B. Biol. Sci., 173, 113, 10.1098/rspb.1969.0043 · doi:10.1098/rspb.1969.0043
  54. Perutz, 1969, Structure and function of hemoglobin, Harvey Lect., 63, 213
  55. Reat, 2000, Solvent dependence of dynamic transitions in protein solutions, Proc. Natl. Acad. Sci. USA, 97, 9961, 10.1073/pnas.97.18.9961 · DOI
  56. Seno, 1990, Deoxymyoglobin studied by the conformational normal mode analysis II. The conformational change upon oxgenation, J. Mol. Biol., 216, 111, 10.1016/S0022-2836(05)80064-6 · doi:10.1016/s0022-2836(05)80064-6
  57. Seno, 1990, Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction, J. Mol. Biol., 216, 95, 10.1016/S0022-2836(05)80063-4 · doi:10.1016/s0022-2836(05)80063-4
  58. Smith, 1991, Protein dynamics: comparison of simulations with inelastic neutron scattering experiments, Q. Rev. Biophys., 24, 227, 10.1017/S0033583500003723 · DOI · Paper page
  59. Smith, 1990, Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra, Proc. Natl. Acad. Sci. USA, 87, 1601, 10.1073/pnas.87.4.1601 · doi:10.1073/pnas.87.4.1601
  60. Suhre, 2004, On the potential of normal-mode analysis for solving difficult molecular-replacement problems, Acta Crystallogr. D Biol. Crystallogr., 60, 796, 10.1107/S0907444904001982 · DOI
  61. Tama, 2002, The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus, J. Mol. Biol., 318, 733, 10.1016/S0022-2836(02)00135-3 · DOI
  62. Tama, 2002, Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory, J. Mol. Biol., 321, 297, 10.1016/S0022-2836(02)00627-7 · DOI · Paper page
  63. Tama, 2003, Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy, Proc. Natl. Acad. Sci. USA, 100, 9319, 10.1073/pnas.1632476100 · DOI · Paper page
  64. Tama, 2004, Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM, J. Struct. Biol., 147, 315, 10.1016/j.jsb.2004.03.002 · DOI · Paper page
  65. Tatsumi, 2004, A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor, J. Comput. Chem., 25, 1995, 10.1002/jcc.20133 · doi:10.1002/jcc.20133
  66. Thirumalai, 2001, Chaperonin-mediated protein folding, Annu. Rev. Biophys. Biomol. Struct., 30, 245, 10.1146/annurev.biophys.30.1.245 · DOI · Paper page
  67. Thomas, 1996, Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase, J. Mol. Biol., 257, 1070, 10.1006/jmbi.1996.0224 · doi:10.1006/jmbi.1996.0224
  68. Thomas, 1996, Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes, J. Mol. Biol., 261, 490, 10.1006/jmbi.1996.0478 · doi:10.1006/jmbi.1996.0478
  69. Thomas, 1999, Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study, Proteins, 34, 96, 10.1002/(SICI)1097-0134(19990101)34:1<96::AID-PROT8>3.0.CO;2-0 · DOI
  70. Tirion, 1996, Large amplitude elastic motions in proteins from a single-parameter, atomic analysis, Phys. Rev. Lett., 77, 1905, 10.1103/PhysRevLett.77.1905 · DOI · Paper page
  71. Tirion, 1995, Normal modes as refinement parameters for the F-actin model, Biophys. J., 68, 5, 10.1016/S0006-3495(95)80156-6 · DOI
  72. Trakhanov, S., Vyas, N.K., Kristensen, D.M., Ma, J., and Quiocho, F.A. (2005). The ligand free and bound structures of the binding protein (LivJ) of the E. coli ABC Leu/Ile/Val transport system: trajectory and dynamics of interdomain rotation and polar versus nonpolar interactions in ligand binding.Biochemistry, in press. · doi:10.1021/bi047302o
  73. Wang, 2004, Global ribosome motions revealed with elastic network model, J. Struct. Biol., 147, 302, 10.1016/j.jsb.2004.01.005 · DOI · Paper page
  74. Wu, 2004, Normal-mode-based refinement of an F-actin model against fibre diffraction data, Fibre Diff. Rev., 12, 25
  75. Wu, 2004, Refinement of F-actin model against fibre diffraction data by long-range normal modes, Biophys. J., 86, 116, 10.1016/S0006-3495(04)74089-8 · doi:10.1016/s0006-3495(04)74089-8
  76. Xu, 1998, GroEL/GroES: structure and function of a two-stroke folding machine, J. Struct. Biol., 124, 129, 10.1006/jsbi.1998.4060 · DOI
  77. Xu, 1997, The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex, Nature, 388, 741, 10.1038/41944 · DOI · Paper page
  78. Xu, 2003, Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T↔R2 transition, J. Mol. Biol., 333, 153, 10.1016/j.jmb.2003.08.027 · DOI · Paper page
  79. Yang, 2003, The missing link between thermodynamics and structure in F1-ATPase, Proc. Natl. Acad. Sci. USA, 100, 874, 10.1073/pnas.0337432100 · doi:10.1073/pnas.0337432100
  80. Zhang, 2003, Molecular dynamics simulations of peptides and proteins with amplified collective motions, Biophys. J., 84, 3583, 10.1016/S0006-3495(03)75090-5 · DOI
  81. Zheng, 2003, A comparative study of motor-protein motions by using a simple elastic-network model, Proc. Natl. Acad. Sci. USA, 100, 13253, 10.1073/pnas.2235686100 · DOI · Paper page
  82. Zhou, 2001, Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The “breathing” core and its functional relationship to protein dynamics, J. Biol. Chem., 276, 21704, 10.1074/jbc.M101765200 · DOI

Cited by

See all 487

Metadata

Authors
Ma, J.
Venue
Structure
Publisher
Elsevier BV
Published
2005-03
Volume
13
Issue
3
Pages
373-380
ISSN
0969-2126 (ISSN-L)
DOI
10.1016/j.str.2005.02.002
OpenAlex
W2051893115
Cited by
487
References
1
FWCI
12.10
Type
journal article
Language
en
Open access
bronze
Licence
Funders
  • National Science Foundation (MCB-0237796)
  • National Institutes of Health (R01-GM067801)
  • National Natural Science Foundation of China

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes. https://app.cochat.ai/papers/10.1016/j.str.2005.02.002
The paper
Ma, J. (2005). Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes. Structure. https://doi.org/10.1016/j.str.2005.02.002

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.