Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models. (1st February 2015)

• Record Type: Journal Article
• Authors: Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.
• Is Part Of: Acta crystallographica. Volume 71:Part 2(2015:Feb.)
• Page Start: 338
• Page End: 343
• Publication Date: 2015-02-01
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S1399004714025784
• Languages: English
• ISSNs: 0907-4449

Abstract

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