Introduction to macromolecular refinement

Methods in Molecular Biology

Volumn 364, Issue , 2007, Pages 231-253

  Tronrud, Dale E ^a  

^a NONE

Author keywords

Crystallography; Least squares refinement; Macromolecular; Maximum likelihood; Refinement

Indexed keywords

ARTICLE; BAYES THEOREM; CHEMICAL STRUCTURE; CHEMISTRY; CRYSTALLOGRAPHY; MACROMOLECULE; METHODOLOGY; STATISTICAL MODEL;

BAYES THEOREM; CRYSTALLOGRAPHY; LIKELIHOOD FUNCTIONS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR;

EID: 36549037602     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-266-1:231     Document Type: Article

References (36)

1. Allen, F. H. (2002) The Cambridge structural database: a quarter of a million crystal structures and rising. Acta Cryst. B58, 380-388.
2. König, V., Vértesy, L., and Schneider, T. R. (2003) Structure of the a-amylase inhibitor tendamistat at 0.93Å. Acta Cryst. D59, 1737-1743.
3. Diamond, R. (1971) A real-space refinement procedure for proteins. Acta Cryst. A27, 436-452.
4. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
5. Stout, G. H. and Jensen, G. H. (1989) X-Ray Structure Determination: A Practical Guide, Second ed. John Wiley and Sons, New York, NY.
6. Kleywegt, G. J. and Jones, T. A. (1995) Where freedom is given, liberties are taken. Structure 3, 535-540.
7. Sheldrick, G. M. and Schneider, T. R. (1997) SHELXL: high-resolution refinement. In: Macromolecular Crystallography, Part B, Vol. 277, (Sweet, R. M. and Carter, Jr, C. W., eds.), Academic Press, New York, NY, pp. 319-343.
8. Rice, L. M. and Brünger, A. (1994) Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Protein: Structure, Function, and Genetics 19, 277-290.
9. Brünger, A. T., Kuriyan, K., and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics. Science 235, 458-460.
10. Brünger, A. T., Adams, P. D., Clore, G. M., et al. (1998) Crystallography and NMR system: a new software system for macromolecular structure determination. Acta Cryst. D54, 905-921.
11. Schomaker, V. and Trueblood, K. N. (1968) On the rigid-body motion of molecules in crystals. Acta Cryst. B24, 63-76.
12. Haneef, I., Moss, D. S., Stanford, M. J., and Borkakoti, N. (1985) Restrained structure-factor least-squares refinement of protein structures using a vector processing computer. Acta Cryst. A41, 426-433.
13. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. D53, 240-255.
14. Winn, M. D., Isupov, M. N., and Murshudov, G. N. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Cryst. D57, 122-133.
15. Levitt, M. (1974) Energy refinement of hen egg-white lysozyme. J. Mol. Biol. 82, 393-420.
16. Konnert, J. H. (1976) A restrained-parameter structure-factor least-squares refinement procedure for large asymmetric units. Acta Cryst. A32, 614-617.
17. Mandel, J. (1984) The Statistical Analysis of Experimental Data. Dover Publications, New York, NY.
18. Bricogne, G. (1988) A Bayesian statistical theory of the phase problem. I. A multichannel maximum-entropy formalism for constructing generalized joint probability distributions of structure factors. Acta Cryst. A44, 517-545.
19. Read, R. J. (1990) Structure-factor probabilities for related structures. Acta Cryst. A46, 900-912.
20. Bricogne, G. (1993) Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives. Acta Cryst. A49, 37-60.
21. Bricogne, G. and Irwin, J. J. (1996) Maximum-likelihood structure refinement: theory and implementation within BUSTER+TNT. In: Macromolecular Refinement: Proceedings of the CCP4 Study Weekend, January 1996, (Dodson, E., Moore, M., Ralph, A., and Bailey, S., eds.), Daresbury Laboratory, Warrington, UK, pp. 85-92.
22. Tronrud, D. E., Ten Eyck, L. F., and Matthews, B. W. (1987) An efficient generalpurpose least-squares refinement program for macromolecular structures. Acta Cryst. A43, 489-501.
23. Bricogne, G. (1997) Bayesian Statistical viewpoint on structure determination: basic concepts and examples. In: Macromolecular Crystallography, Part A, Vol. 276, (Sweet, R. M. and Carter, Jr., C. W., eds.), Academic Press, New York, NY, pp. 361-423.
24. Sivia, D. S. (1996) Data Analysis: A Bayesian Tutorial. Oxford University Press, Oxford, UK.
25. Wilson, A. J. C. (1942) Determination of absolute from relative X-ray intensity data. Nature 150, 151-152.
26. Wilson, A. J. C. (1949) The probability distribution of X-ray intensities. Acta Cryst. 2, 318-321.
27. Pannu, N. S. and Read, R. J. (1996) Improved structure refinement through maximum likelihood. Acta Cryst. A52, 659-669.
28. Srinivansan, R. and Parthasarathy, S. (176) Some Statistical Applications in X-ray Crystallography, Pergamon Press, Oxford, UK.
29. Read, R. J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A42, 140-149.
30. Brünger, A. T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
31. Roversi, P., Blanc, E., Vonrhein, C., Evans, G., and Bricogne, G. (2000) Modelling prior distributions of atoms for macromolecular refinement and completion Acta Cryst. D56, 1316-1323.
32. Krikpatrick, Jr., S., Gelatt, C. D., and Vecchi, M. P. (1983) Optimization by simulated annealing. Science 220, 671-680.
33. Otten, R. H. J. M. and van Ginneken, L. P. P. P. (1989) The Annealing Algorithm, Kluwer Academic Publishers, Boston, MA.
34. Fletcher, R. and Reeves, C. (1964) Function minimization by conjugate gradients. Computer Journal 1, 81-84.
35. Axelsson, O. and Barker, V. A. (1984) Quadratic functionals on finite-dimensional vector spaces. In: Finite Element Solution of Boundary Value Problems, Academic Press, Inc., Orlando, FL, pp. 1-63.
36. Tronrud, D. E. (1992) Conjugate-direction minimization: an improved method for the refinement of macromolecules. Acta Cryst. A48, 912-916.