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Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):338-43. doi: 10.1107/S1399004714025784. Epub 2015 Jan 23.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

Author information

1
Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England.
2
Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England.
3
Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
4
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
5
Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD, England.

Abstract

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

KEYWORDS:

AMPLE; QUARK; ROSETTA; ab initio modelling; molecular replacement

PMID:
25664744
PMCID:
PMC4321487
DOI:
10.1107/S1399004714025784
[Indexed for MEDLINE]
Free PMC Article

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