Modeling supramolecular assemblages

Current Opinion in Structural Biology

Volumn 12, Issue 2, 2002, Pages 154-160

  Elcock, Adrian H ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AQUAPORIN 1; GLYCEROL; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

ACCURACY; CALCULATION; COMPUTER SIMULATION; CONFORMATION; CRYOELECTRON MICROSCOPY; ELECTRICITY; ELECTRON MICROSCOPY; FEASIBILITY STUDY; MACROMOLECULE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW; SUPRAMOLECULAR CHEMISTRY; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

EID: 0036536969     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00303-2     Document Type: Review

References (56)

1. Molecular machines: Putting the pieces together
2. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
3. Structure of the 30A ribosomal subunit
4. Atomic structures at last: The ribosome in 2000
5. Fitting atomic models into electron-microscopy maps
6. Atomic model of the actin filament
7. Modeling tricks and fitting techniques for multiresolution structures
8. Using Situs for flexible and rigid-body fitting of multi-resolution single molecule data
9. Between objectivity and subjectivity
10. Quality assessment of NMR structures: A statistical survey
11. Prediction of protein-protein interactions by docking methods
12. Computer simulation of protein-protein interactions
13. The middle way
14. Functional dynamics in the active site of the ribonuclease binase
15. Protein dynamics from NMR
16. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules
17. Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy
18. New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations
19. Nucleic acids: Theory and computer simulation, Y2K
20. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study
21. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation
22. Targeted molecular dynamics simulation of conformational change: Application to the T-R transition in insulin
23. Stretching single molecules into novel conformations using the atomic force microscope
24. Steered molecular dynamics and mechanical functions of proteins
25. Nonequilibrium equality for free energy differences
26. How does a system respond when driven away from thermal equilibrium?
27. A 'fast growth' method of computing free energy differences
28. Free energy reconstruction from nonequilibrium single-molecule pulling experiments
29. A dynamic model for the allosteric mechanism of GroEL
30. Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
31. Analysis of domain motions by approximate normal mode calculations
32. Collective protein dynamics in relation to function
33. Anisotropy of fluctuation dynamics of proteins with an elastic network model
34. Classical electrostatics in biology and chemistry
35. Electrostatics of nanosystems: Application to microtubules and the ribosome
36. Calculation of the total electrostatic energy of a macromolecular system; solvation energies, binding energies and conformational analysis
37. Computational modeling predicts the structure and dynamics of chromatin fiber
38. DNA packaging and ejection forces in bacteriophage
39. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
40. Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III
41. Long timescale simulations
42. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
43. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
44. Thermodynamic insights into proteins from NMR spin relaxation studies
45. Studying excited states of proteins by NMR spectroscopy
46. Protein dynamic studies move to a new time slot
47. Engineering the processive run-length of the kinesin motor
48. What are the dielectric 'constants' of proteins and how to validate electrostatic models?
49. To charge or not to charge?
50. Effective charges for macromolecules in solvent
51. + channel
52. Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF
53. Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase
54. Ultrafast folding of WW domains without structured aromatic clusters in the denatured state