Tuesday, May 13th at 12:00pm EDT -- please join our webinar to hear the latest on Refinement of challenging structures with Rosetta and Phenix. Nathaniel Echols, Computational Scientist at Lawrence Berkeley National Labs, will present.
Nathaniel Echols, Ph.D.
Lawrence Berkeley National Labs
Refinement of macromolecular structures against low-resolution crystallographic data is limited by the ability of current methods to converge on a structure with realistic geometry. We developed a low-resolution crystallographic refinement method that combines the Rosetta sampling methodology and energy function with reciprocal-space X-ray refinement in Phenix. On a set of difficult low-resolution cases, the method yielded improved model geometry and lower free R factors than alternate refinement methods.
For more information on Phenix-Rosetta refinement, check out the website or read one of these papers of interest:
- Improved low-resolution crystallographic refinement with Phenix and Rosetta. F. DiMaio, N. Echols, J.J. Headd, T.C. Terwilliger, P.D. Adams, and D.A. Baker. Nature Methods in press (2013). Abstract
- Towards automated crystallographic structure refinement with phenix.refine. P.V. Afonine, R.W. Grosse-Kunstleve, N. Echols, J.J. Headd, N.W. Moriarty, M. Mustyakimov, T.C. Terwilliger, A. Urzhumtsev, P.H. Zwart, and P.D. Adams. Acta Cryst. D68, 352-367 (2012).Abstract
- Correcting pervasive errors in RNA crystallography through enumerative structure prediction. F.C. Chou, P. Sripakdeevong, S.M. Dibrov, T. Hermann, and R. Das. Nature Methods 10, 74-76 (2012).Abstract
- Improving molecular replacement by density and energy guided protein structure optimization. F. DiMaio, T.C. Terwilliger, R.J. Read, A. Wlodawer, G. Oberdorfer, U. Wagner, E. Valkov, A. Alon, D. Fass, H.L. Axelrod, D. Das, S.M. Vorobiev, H. Iwai, P.R. Pokkuluri, and D. Baker. Nature 473, 540-543 (2011). Abstract
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