Enhanced macromolecular refinement by simulated annealing
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
ch. 18.2,
pp. 466-473
[ doi:10.1107/97809553602060000856 ]
a stepping stone towards development of improved models of macromolecules in solution and in the crystalline state.
The computational developments discussed in this review are implemented in the software suite Crystallography & NMR System (
Brunger ...
Searching conformational space
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
Section 18.2.4,
pp. 468-470
[ doi:10.1107/97809553602060000856 ]
(1984). Molecular dynamics with coupling to an external bath. J. Chem. Phys . 81, 3684–3690. Google Scholar
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[
more
results from section 18.2.4 in volume F]
Conclusions
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
Section 18.2.8,
pp. 472-472
[ doi:10.1107/97809553602060000856 ]
are implemented in the software suite Crystallography & NMR System (
Brunger et al., 1998). A pre-release of the software suite is available upon request.
References
Adams, P. D., Pannu, N. S., Read, R. J. & Brünger ...
A priori chemical information
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
Section 18.2.3.2,
pp. 468-468
[ doi:10.1107/97809553602060000856 ]
Vojtechovsky, J., Clowney, L.,
Brunger, A. T. & Berman, H. M. (1996). New parameters for the refinement of nucleic acid-containing structures. Acta Cryst . D 52, 57–64. Google Scholar
Pearlman, D. A. & Kim, S.-H. (1990). Atomic ...
[
more
results from section 18.2.3 in volume F]
Introduction
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
Section 18.2.1,
pp. 466-466
[ doi:10.1107/97809553602060000856 ]
Google Scholar
Brunger, A. T. (1992). The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature (London), 355, 472–474. Google Scholar
Brunger, A. T., Kuriyan, J. & Karplus ...
Ensemble models
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
Section 18.2.7,
pp. 471-472
[ doi:10.1107/97809553602060000856 ]
conformer refinement requires a high observable-to-parameter ratio.
References
Burling, F. T. &
Brunger, A. T. (1994). Thermal motion and conformational disorder in protein crystal structures: comparison of multi-conformer ...
Examples
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
Section 18.2.5,
pp. 470-471
[ doi:10.1107/97809553602060000856 ]
–5023. Google Scholar
Adams, P. D., Pannu, N. S., Read, R. J. &
Brunger, A. T. (1999). Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement. Acta Cryst . D 55, 181 ...
Multi-start refinement and structure-factor averaging
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
Section 18.2.6,
pp. 471-471
[ doi:10.1107/97809553602060000856 ]
in situations where there is significant noise, namely when the data-to-parameter ratio is low (e.g. if only moderate-resolution diffraction data are available).
References
Brunger, A. T. (1988). Crystallographic refinement ...
Cross validation
Brunger, A. T.,
Adams, P. D. and
Rice, L. M.,
International Tables for Crystallography
(2012).
Vol. F,
Section 18.2.2,
pp. 466-467
[ doi:10.1107/97809553602060000856 ]
Cross-validated coordinate-error estimates. The test set was used to compute the coordinate-error estimates (Kleywegt & Brünger, 1996).
References
Brunger, A. T. (1992). The free R value: a novel statistical ...
CNS, a program system for structure-determination and refinement
Brunger, A. T.,
Adams, P. D.,
DeLano, W. L.,
Gros, P.,
Grosse-Kunstleve, R. W.,
Jiang, J.-S.,
Pannu, N. S.,
Read, R. J.,
Rice, L. M. and
Simonson, T.,
International Tables for Crystallography
(2012).
Vol. F,
ch. 18.6,
pp. 512-519
[ doi:10.1107/97809553602060000860 ]
Brünger et al. (1997) .
During simulated-annealing refinement, the model can be significantly improved. Therefore, it becomes important to recalculate the cross-validated error estimates (Kleywegt &
Brunger, 1996 ; Read, 1997 ...
