DOI: 10.1126/science.1110428. Inferential Structure Determination

10.1126/science.1110428

Crossref journal-article

American Association for the Advancement of Science (AAAS)

Science (221)

Abstract

Macromolecular structures calculated from nuclear magnetic resonance data are not fully determined by experimental data but depend on subjective choices in data treatment and parameter settings. This makes it difficult to objectively judge the precision of the structures. We used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision. This probability distribution also determines additional unknowns, such as theory parameters, that previously had to be chosen empirically. We implemented this approach by using Markov chain Monte Carlo techniques. Our method provides an objective figure of merit and improves structural quality.

Bibliography

Rieping, W., Habeck, M., & Nilges, M. (2005). Inferential Structure Determination. Science, 309(5732), 303â306.

Authors 3

Wolfgang Rieping (first)
Michael Habeck (additional)
Michael Nilges (additional)

References 26 Referenced 318

S. Macura, R. R. Ernst, Mol. Phys.41, 95 (1980). (10.1080/00268978000102601) / Mol. Phys. (1980)
A. T. Brünger, M. Nilges, Q. Rev. Biophys.26, 49 (1993). (10.1017/S0033583500003966) / Q. Rev. Biophys. (1993)
R. T. Cox, Am. J. Phys.14, 1 (1946). (10.1119/1.1990764) / Am. J. Phys. (1946)
E. T. Jaynes Probability Theory: The Logic of Science (Cambridge Univ. Press Cambridge 2003). (10.1017/CBO9780511790423)
Materials and methods are available as supporting material on Science Online.
T. K. Mal, S. J. Matthews, H. Kovacs, I. D. Campbell, J. Boyd, J. Biomol. NMR12, 259 (1998). (10.1023/A:1008238009056) / J. Biomol. NMR (1998)
10.1021/ja00381a009
R. H. Swendsen, J.-S. Wang, Phys. Rev. Lett.57, 2607 (1986). (10.1103/PhysRevLett.57.2607) / Phys. Rev. Lett. (1986)
M. Habeck, M. Nilges, W. Rieping, Phys. Rev. Lett.94, 0181051 (2005). / Phys. Rev. Lett. (2005)
M. E. Noble, A. Musacchio, M. Saraste, S. A. Courtneidge, R. K. Wierenga, EMBO J.12, 2617 (1993). (10.1002/j.1460-2075.1993.tb05922.x) / EMBO J. (1993)
10.1038/355472a0
10.1126/science.8332897
P. D. Adams, N. S. Pannu, R. J. Read, A. T. Brünger, Proc. Natl. Acad. Sci. U.S.A.94, 5018 (1997). (10.1073/pnas.94.10.5018) / Proc. Natl. Acad. Sci. U.S.A. (1997)
M. H. Chen Q. M. Shao J. G. Ibrahim Monte Carlo Methods in Bayesian Computation (Springer Verlag New York 2002).
R. B. Altman, O. Jardetzky, Methods Enzymol.177, 218 (1989). (10.1016/0076-6879(89)77013-0) / Methods Enzymol. (1989)
M. Andrec, G. T. Montelione, R. M. Levy, J. Magn. Reson.139, 408 (1999). (10.1006/jmre.1999.1839) / J. Magn. Reson. (1999)
G. Bricogne, Methods Enzymol.276, 361 (1997). (10.1016/S0076-6879(97)76069-5) / Methods Enzymol. (1997)
M. Karplus, J. Am. Chem. Soc.85, 2870 (1963). (10.1021/ja00901a059) / J. Am. Chem. Soc. (1963)
W. Rieping M. Habeck M. Nilges data not shown.
S. Geman, D. Geman, IEEE Trans. Pattern Anal. Mach. Intell.6, 721 (1984). / IEEE Trans. Pattern Anal. Mach. Intell. (1984)
S. Duane, A. D. Kennedy, B. Pendleton, D. Roweth, Phys. Lett. B195, 216 (1987). (10.1016/0370-2693(87)91197-X) / Phys. Lett. B (1987)
M. Nilges, M. J. Macias, S. I. O'Donoghue, H. Oschkinat, J. Mol. Biol.269, 408 (1997). (10.1006/jmbi.1997.1044) / J. Mol. Biol. (1997)
10.1107/S0907444998003254
10.1016/0263-7855(96)00009-4
M. Nilges, S. I. O'Donoghue, Prog. Nucl. Magn. Reson. Spectrosc.32, 107 (1998). (10.1016/S0079-6565(97)00025-3) / Prog. Nucl. Magn. Reson. Spectrosc. (1998)
The authors thank I. D. Campbell for kindly providing the experimental SH3 NMR data. This work was supported by European Union grants QLG2-CT-2000-01313 and QLG2-CT-2002-00988. The 20 most likely structures and the restraint list used in the calculation have been deposited in the Protein Data Bank under accession code 1ZBJ. The structure determination program is available from the authors on request to M.N.

Dates

Type	When
Created	20 years, 1 month ago (July 7, 2005, 4:48 p.m.)
Deposited	1 year, 7 months ago (Jan. 9, 2024, 10:02 p.m.)
Indexed	2 weeks, 6 days ago (Aug. 2, 2025, 12:07 a.m.)
Issued	20 years, 1 month ago (July 8, 2005)
Published	20 years, 1 month ago (July 8, 2005)
Published Print	20 years, 1 month ago (July 8, 2005)

Funders 0

None

BibTeX

@article{Rieping_2005, title={Inferential Structure Determination}, volume={309}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1110428}, DOI={10.1126/science.1110428}, number={5732}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Rieping, Wolfgang and Habeck, Michael and Nilges, Michael}, year={2005}, month=jul, pages={303–306} }

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