Molecular dynamics applied to X-ray structure refinement

Accounts of Chemical Research

Volumn 35, Issue 6, 2002, Pages 404-412

  Brunger, Axel T ^a   Adams, Paul D ^b  

^a SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONFORMATION; CRYSTALLOGRAPHY; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; TEMPERATURE; X RAY DIFFRACTION; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METHODOLOGY; MOTION; REVIEW;

BIOPOLYMER;

BIOPOLYMERS; COMPUTER SIMULATION; MOLECULAR STRUCTURE; MOTION; TEMPERATURE; X-RAY DIFFRACTION;

EID: 0036280741     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar010034r     Document Type: Article

References (67)

1. Cool data: Quantity and quality
2. MAD data collection-current trends
3. Taking MAD to the extreme: Ultrafast protein structure determination
4. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation
5. Optimization by simulated annealing
6. Crystallographic R factor refinement by molecular dynamics
7. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
8. Structure of the 30S ribosomal subunit
9. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution
10. The free R value: A novel statistical quantity for assessing the accuracy of crystal structures
11. Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement
12. Improved structure refinement through maximum likelihood
13. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement
14. Incorporation of prior phase information strengthens maximum likelihood structural refinement
15. Exploration of disorder in protein structures by X-ray restrained molecular dynamics
16. Thermal motion and conformational disorder in protein crystal structures: Comparison of multi-conformer and time-averaging models
17. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases
18. Stereochemically restrained refinement of macromolecular structures
19. Accurate bond and angle parameters for x-ray structure refinement
20. New parameters for the refinement of nucleic acid containing structures
21. Systematic analysis of structural data as a research technique in organic chemistry
22. Proteins at atomic resolution
23. Full-matrix refinement of the protein crambin at 0.83 Å and 130 K
24. Ribonuclease from Streptomyces aureofaciens at atomic resolution
25. Structural parameters for proteins derived from the atomic resolution (1.09 Å) structure of a designed variant of the coE1 ROP protein
26. Atomic charges for DNA constituents derived from single-crystal x-ray diffraction data
27. Molecular dynamics simulations in biology
28. Crystallographic refinement by simulated annealing: Application to a 1.5 Å resolution structure of crambin
29. Refinement of the influenza virus haemagglutinin by simulated annealing
30. Slow-cooling protocols for crystallographic refinement by simulated annealing
31. Testing the method of crystallographic refinement using molecular dynamics
32. The refinement of southern bean mosaic virus in reciprocal space
33. Improved Fourier coefficients for maps using phases from partial structures with errors
34. Structure-factor probabilities for related structures
35. A multisolution method of phase determination by combined maximization of entropy and likelihood. III. Extension to powder diffraction data
36. Direct phase determination by entropy maximization and likelihood ranking: Status report and perspectives
37. Refinement of macromolecular structures by the maximum-likelihood method
38. Cross-validation in crystallography: Practice and applications
39. Extending the limits of molecular replacement through combined simulated annealing and maximum likelihood refinement
40. Bayesian statistical viewpoints on structure determination: Basic concepts and examples
41. Single wavelength anomalous diffraction phasing revisited
42. A real-space refinement procedure for proteins
43. Structure-factor least-squares refinement procedure for macro-molecular structure using constrained and restrained parameters
44. Equation of state calculations by fast computing machines
45. Computer experiments on classical fluids. I. Thermo-dynamical properties of Lennard-Jones molecules
46. A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems
47. A recursive formulation for constrained mechanical system dynamics. Part II. Closed loop systems
48. A fast recursive algorithm for molecular dynamics simulation
49. Protein simulations using techniques suitable for very large systems: The cell mulipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics
50. Molecular dynamics with coupling to an external bath
51. Crystallographic refinement by simulated annealing: Application to a 2.8 Å resolution structure of aspartate aminotransferase
52. Die faltmolekülmethode-eine neue methode zur bestimmung der kristallstruktur bei ganz oder teilweise bekannter Molekülstruktur
53. The detection of subunits within the crystallographic asymmetric unit
54. Model bias in macromolecular crystal structures
55. Crystal structure of the two RNA-binding domains of human hnRNP A1 at 1.75 Å resolution
56. Phase improvement by multi-start simulated annealing refinement and structure factor averaging
57. Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics
58. Effect of anisotropy and anharmonicity on protein crystallographic refinement
59. 2+ bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity
60. Recent developments in software for automation of crystallographic macromolecular structure determination
61. Crystallography & NMR system (CNS): A new software system for macromolecular structure determination
62. Penicillopepsin from Penicillium janthinellum crystal structure at 2.8 Å and sequence homology with porcine pepsin
63. X-ray analyses of aspartic proteinases. V. Structure and refinement at 2.0 Å resolution of the aspartic proteinase from Mucor pusillus