Crossref journal-article
Elsevier BV
Current Opinion in Structural Biology (78)
Bibliography

Ayton, G. S., Noid, W. G., & Voth, G. A. (2007). Multiscale modeling of biomolecular systems: in serial and in parallel. Current Opinion in Structural Biology, 17(2), 192–198.

Authors 3
  1. Gary S Ayton (first)
  2. Will G Noid (additional)
  3. Gregory A Voth (additional)
References 81 Referenced 375
  1. 10.1038/nsb0902-646 / Nat Struct Biol / Molecular dynamics simulations of biomolecules by Karplus (2002)
  2. 10.1016/S1359-0294(00)00058-3 / Curr Opin Colloid Interface Sci / Molecular dynamics simulations of lipid bilayers by Feller (2000)
  3. 10.1007/s00249-005-0013-y / Eur Biophys J / Implicit solvent simulation models for biomembranes by Brannigan (2006)
  4. 10.1063/1.476160 / J Chem Phys / Computer simulations of bilayer membranes: self-assembly and interfacial tension by Goetz (1998)
  5. 10.1063/1.1814058 / J Chem Phys / Coarse-grained simulations of lipid bilayers by Stevens (2004)
  6. 10.1021/jp010238p / J Phys Chem B / A coarse grain model for phospholipid simulation by Shelley (2001)
  7. {'key': '10.1016/j.sbi.2007.03.004_bib7', 'first-page': '9792', 'article-title': 'Simulation of phospholipids using a coarse grain model', 'volume': '105', 'author': 'Shelley', 'year': '2001', 'journal-title': 'J Phys Chem B'} / J Phys Chem B / Simulation of phospholipids using a coarse grain model by Shelley (2001)
  8. 10.1021/jp036508g / J Phys Chem B / Coarse grained model for semiquantitative lipid simulations by Marrink (2004)
  9. 10.1021/ja036138+ / J Am Chem Soc / The mechanism of vesicle fusion as revealed by molecular dynamics simulations by Marrink (2003)
  10. 10.1021/jp0550816 / J Phys Chem B / Coarse grained protein–lipid model with applications to lipoprotein particles by Shih (2006)
  11. 10.1063/1.1625913 / J Chem Phys / Solvent-free simulations of membrane bilayers by Brannigan (2004)
  12. 10.1103/PhysRevE.72.011506 / Phys Rev E Stat Nonlin Soft Matter Phys / Tunable generic model of fluid bilayer membranes by Cooke (2005)
  13. 10.1063/1.1578612 / J Chem Phys / ‘Water-free’ computer model for fluid bilayer membranes by Farago (2003)
  14. 10.1007/s00249-005-0005-y / Eur Biophys J / Multiscale modeling of lipids and lipid bilayers by Lyubartsev (2005)
  15. 10.1021/jp044629q / J Phys Chem B / A multiscale coarse-graining method for biomolecular systems by Izvekov (2005)
  16. 10.1021/ct050300c / J Chem Theor Comp / Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers by Izvekov (2006)
  17. 10.1016/j.jsb.2006.10.020 / J Struct Biol / Multiscale simulation of transmembrane proteins by Ayton (2007)
  18. 10.1021/jp062700h / J Phys Chem B / Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane bound ion channel by Shi (2006)
  19. 10.1016/j.sbi.2005.02.005 / Curr Opin Struct Biol / Coarse-grained models for proteins by Tozzini (2005)
  20. 10.1038/253694a0 / Nature / Computer simulation of protein folding by Levitt (1975)
  21. 10.1016/0022-2836(76)90004-8 / J Mol Biol / A simplified representation of protein conformations for rapid simulation of protein folding by Levitt (1976)
  22. 10.1021/ma60054a013 / Macromolecules / Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins by Tanaka (1976)
  23. 10.1021/ma00145a039 / Macromolecules / Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation by Miyazawa (1985)
  24. 10.1016/S0022-2836(05)80269-4 / J Mol Biol / Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins by Sippl (1990)
  25. 10.1063/1.1561616 / J Chem Phys / Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures by Buchete (2003)
  26. 10.1002/jcc.20286 / J Comput Chem / Protein structure prediction with the UNRES force-field using replica-exchange Monte Carlo-with-minimization; comparison with MCM, CSA, and CFMC by Nanias (2005)
  27. 10.1021/ct050253o / J Chem Theory Comput / Replica exchange and multicanonical algorithms with the coarse-grained united-residue (UNRES) force field by Nanias (2006)
  28. 10.1016/S0959-440X(96)80075-3 / Curr Opin Struct Biol / Structure-derived potential and protein simulations by Jernigan (1996)
  29. 10.1063/1.477748 / J Chem Phys / Pairwise contact potentials are unsuitable for protein folding by Vendruscolo (1998)
  30. 10.1063/1.1383989 / J Chem Phys / Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field by Liwo (2001)
  31. 10.1016/j.jmb.2004.08.006 / J Mol Biol / Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go? by Matysiak (2004)
  32. 10.1002/prot.340210302 / Proteins / Funnels, pathways, and the energy landscape of protein folding: a synthesis by Bryngelson (1995)
  33. 10.1146/annurev.bb.12.060183.001151 / Annu Rev Biophys Bioeng / Theoretical studies of protein folding by Go (1983)
  34. 10.1073/pnas.072665799 / Proc Natl Acad Sci USA / A structure-based method for derivation of all-atom potentials for protein folding by Kussell (2002)
  35. 10.1002/prot.10429 / Proteins / Optimizing physical energy functions for protein folding by Fujitsuka (2004)
  36. 10.1016/j.jmb.2005.05.017 / J Mol Biol / Reconstruction of the Src–SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations by Ding (2005)
  37. 10.1103/PhysRevLett.77.1905 / Phys Rev Lett / Large amplitude elastic motions in proteins from a single-parameter, atomic analysis by Tirion (1996)
  38. 10.1103/PhysRevLett.79.3090 / Phys Rev Lett / Gaussian dynamics of folded proteins by Haliloglu (1997)
  39. 10.1016/S0006-3495(01)76033-X / Biophys J / Anisotropy of fluctuation dynamics of proteins with an elastic network model by Atilgan (2001)
  40. 10.1529/biophysj.106.083568 / Biophys J / A natural coarse graining for simulating large biomolecular motion by Gohlke (2006)
  41. 10.1016/S0006-3495(04)74089-8 / Biophys J / Refinement of F-actin model against fiber diffraction data by long-range normal modes by Wu (2004)
  42. 10.1073/pnas.232588999 / Proc Natl Acad Sci USA / Substructure synthesis method for simulating large molecular complexes by Ming (2003)
  43. 10.1016/S0006-3495(95)80156-6 / Biophys J / Normal modes as refinement parameters for the F-actin model by Tirion (1995)
  44. 10.1016/j.jmb.2005.02.027 / J Mol Biol / The 13Å structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy by Falke (2005)
  45. 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)
  46. 10.1021/ct600060d / J Chem Theory Comput / The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models by Sen (2006)
  47. 10.1021/bi0518085 / Biochemistry / Loop motions of triosephosphate isomerase observed with elastic networks by Kurkcuoglu (2006)
  48. 10.1016/S0006-3495(03)75090-5 / Biophys J / Molecular dynamics simulations of peptides and proteins with amplified collective modes by Zhang (2003)
  49. 10.1073/pnas.75.2.559 / Proc Natl Acad Sci USA / Respective roles of short- and long-range interactions in protein folding by Go (1978)
  50. 10.1073/pnas.162268099 / Proc Natl Acad Sci USA / The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation by Shimada (2002)
  51. 10.1103/PhysRevLett.95.218102 / Phys Rev Lett / Coarse-grained model of proteins incorporating atomistic detail of the active site by Neri (2005)
  52. 10.1073/pnas.1931882100 / Proc Natl Acad Sci USA / Coarse-grained sequences for protein folding and design by Brown (2003)
  53. 10.1021/jp0370730 / J Phys Chem B / Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin by Zuckerman (2004)
  54. 10.1073/pnas.0603557103 / Proc Natl Acad Sci USA / Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation by Swigon (2006)
  55. 10.1021/ct050307u / J Chem Theory Comput / A new method for coarse-grained elastic normal-mode analysis by Lu (2006)
  56. 10.1016/j.jmb.2006.07.088 / J Mol Biol / Minimalist protein model as a diagnostic tool for misfolding and aggregation by Matysiak (2006)
  57. 10.1529/biophysj.105.073924 / Biophys J / Coarse-grained modeling of the actin filament derived from atomistic-scale simulations by Chu (2006)
  58. 10.1073/pnas.0503732102 / Proc Natl Acad Sci USA / Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis by Chu (2005)
  59. 10.1103/PhysRevLett.96.028105 / Phys Rev Lett / Resolution exchange simulation by Lyman (2006)
  60. 10.1021/ct050337x / J Chem Theory Comput / Resolution exchange simulation with incremental coarsening by Lyman (2006)
  61. 10.1063/1.2408415 / J Chem Phys / Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes by Liu (2007)
  62. 10.1063/1.1833354 / J Chem Phys / Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials by Giessen (2005)
  63. 10.1021/ct0503318 / J Chem Theory Comput / Coarse-grained model of coil-to-helix kinetics demonstrates the importance of multiple nucleation sites in helix folding by van Giessen (2006)
  64. 10.1103/PhysRevE.69.041908 / Phys Rev E Stat Nonlin Soft Matter Phys / Discrete molecular dynamics simulations of peptide aggregation by Peng (2004)
  65. Zhou J, Thorpe IF, Izvekov S, Voth GA: Coarse-grained peptide modeling using a systematic multiscale approach. Biophys J 2007, in press. (10.1529/biophysj.106.094425)
  66. 10.1073/pnas.0409387102 / Proc Natl Acad Sci USA / Structural dynamics of the lac repressor–DNA complex revealed by a multiscale simulation by Villa (2005)
  67. 10.1137/040604789 / Multiscale Model Simul / Multiscale method for simulating protein-DNA complexes by Villa (2004)
  68. 10.1002/bip.10529 / Biopolymers / Packaging double-helical DNA into viral capsids by LaMarque (2004)
  69. 10.1016/j.str.2006.11.013 / Structure / Structural and thermodynamic principles of viral packaging by Petrov (2007)
  70. 10.1016/S0006-3495(99)77074-8 / Biophys J / From atomic to mesoscopic descriptions of the internal dynamics of DNA by Bruant (1999)
  71. 10.1073/pnas.0408867102 / Proc Natl Acad Sci USA / Electrostatic mechanism of nucleosomal array folding revealed by computer simulation by Sun (2005)
  72. 10.1021/ct049950r / J Chem Theory Comput / Normal-mode analysis of circular DNA at the base-pair level. 1. Comparison of computed motions with the predicted behavior of an ideal elastic rod by Matsumoto (2005)
  73. 10.1021/ct049949s / J Chem Theory Comput / Normal-mode analysis of circular DNA at the base-pair level. 2. Large-scale configurational transformation of a naturally curved molecule by Matsumoto (2005)
  74. 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)
  75. 10.1016/j.jsb.2004.01.005 / J Struct Biol / Global ribosome motions revealed with elastic network model by Wang (2004)
  76. 10.1529/biophysj.105.064840 / Biophys J / Comparison of tRNA motions in the free and ribosomal bound structures by Wang (2005)
  77. 10.1063/1.1739396 / J Chem Phys / Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching by Izvekov (2004)
  78. Noid WG, Chu J-W, Ayton GS, Voth GA: Multiscale coarse-graining and structural correlations: connections to liquid state theory. J Phys Chem B 2007, in press. (10.1021/jp068549t)
  79. 10.1063/1.2360580 / J Chem Phys / Modeling real dynamics in the coarse-grained representations of condensed phase systems by Izvekov (2006)
  80. 10.1063/1.480476 / J Chem Phys / Effective potentials for ion-DNA interactions by Lyubartsev (1999)
  81. 10.1063/1.2165194 / J Chem Phys / A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics by Ayton (2005)
Dates
Type When
Created 18 years, 4 months ago (March 24, 2007, 7:06 a.m.)
Deposited 6 years, 7 months ago (Jan. 8, 2019, 12:23 p.m.)
Indexed 3 weeks, 4 days ago (July 28, 2025, 2:52 a.m.)
Issued 18 years, 4 months ago (April 1, 2007)
Published 18 years, 4 months ago (April 1, 2007)
Published Print 18 years, 4 months ago (April 1, 2007)
Funders 0

None

@article{Ayton_2007, title={Multiscale modeling of biomolecular systems: in serial and in parallel}, volume={17}, ISSN={0959-440X}, url={http://dx.doi.org/10.1016/j.sbi.2007.03.004}, DOI={10.1016/j.sbi.2007.03.004}, number={2}, journal={Current Opinion in Structural Biology}, publisher={Elsevier BV}, author={Ayton, Gary S and Noid, Will G and Voth, Gregory A}, year={2007}, month=apr, pages={192–198} }