phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta
By T. C. Terwilliger, Frank DiMaio, Randy J. Read, David Baker, G. Bunkoczi, Paul D. Adams, R. Grosse-Kunstleve, Pavel V. Afonine, Nathaniel Echols. 2012
135 citations recorded by the source corpus.
The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement.
Subfields: Materials Chemistry, Physical and Theoretical Chemistry
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Paul D. Adams
- Pavel V. Afonine
- Randy J. Read
- T. C. Terwilliger
- Nigel W. Moriarty
- T. Croll
- A. McCoy
- Jane S. Richardson
In Physical and Theoretical Chemistry
- Randy J. Read
- M. Sammito
- T. Croll
- Pavel V. Afonine
- Alexandre Urzhumtsev
- A. McCoy
- Paul D. Adams
- T. C. Terwilliger
Citations in the corpus
- Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “D75, 861–877 (i) MR-Rosetta (phenix.mr_rosetta) uses homology modeling in the Rosetta program to improve a model before and/or after MR (DiMaio et al., 2011; Terwilliger et al., 2012).”
- Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “A similar idea has already been implemented by other laboratories via the integration of electron-density information with Rosetta modeling (DiMaio et al., 2011; Terwilliger et al., 2012).”
- Automatically fixing errors in glycoprotein structures with Rosetta (2018, methodology): “, 2016) and X-ray crystallography data, the latter taking advantage of the combined Phenix-Rosetta reciprocal-space refinement pipeline (Terwilliger et al., 2012).”