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

Keegan RM, Bibby J, Thomas J, Xu D, Zhang Y, Mayans O, Winn MD, Rigden DJ - Acta Crystallogr. D Biol. Crystallogr. (2015)

Bottom Line: AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, 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.

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Related in: MedlinePlus

Numbers of targets solved with QUARK-derived search models under various conditions compared with previous results (Bibby et al., 2012 ▶). The small numbers at the top left of the columns indicate the run numbers referred to in the text.
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fig1: Numbers of targets solved with QUARK-derived search models under various conditions compared with previous results (Bibby et al., 2012 ▶). The small numbers at the top left of the columns indicate the run numbers referred to in the text.

Mentions: ROSETTA-derived search models processed with Phaser previously solved 126 of the 295 targets. The result for the QUARK set, using the same Phaser and SHELXE versions and operating parameters, is 100/295 (Run 1). As previously (Bibby et al., 2012 ▶), when producing the QUARK models homologous fragments were excluded to treat each target as if it were a novel fold. For comparison we also tested providing Phaser with a 1.2 Å estimated r.m.s. error in the search models (Run 2), as opposed to the 0.1 Å value employed in Run 1. This dramatically reduced the success rate to 70/295 and thus the value of 0.1 Å was used for all of the remaining runs. We then tested the success of the QUARK models using the latest versions of Phaser and SHELXE (Run 3) and found a steep increase in success to 126 of the 295 cases (Fig. 1 ▶).


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

Keegan RM, Bibby J, Thomas J, Xu D, Zhang Y, Mayans O, Winn MD, Rigden DJ - Acta Crystallogr. D Biol. Crystallogr. (2015)

Numbers of targets solved with QUARK-derived search models under various conditions compared with previous results (Bibby et al., 2012 ▶). The small numbers at the top left of the columns indicate the run numbers referred to in the text.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4321487&req=5

fig1: Numbers of targets solved with QUARK-derived search models under various conditions compared with previous results (Bibby et al., 2012 ▶). The small numbers at the top left of the columns indicate the run numbers referred to in the text.
Mentions: ROSETTA-derived search models processed with Phaser previously solved 126 of the 295 targets. The result for the QUARK set, using the same Phaser and SHELXE versions and operating parameters, is 100/295 (Run 1). As previously (Bibby et al., 2012 ▶), when producing the QUARK models homologous fragments were excluded to treat each target as if it were a novel fold. For comparison we also tested providing Phaser with a 1.2 Å estimated r.m.s. error in the search models (Run 2), as opposed to the 0.1 Å value employed in Run 1. This dramatically reduced the success rate to 70/295 and thus the value of 0.1 Å was used for all of the remaining runs. We then tested the success of the QUARK models using the latest versions of Phaser and SHELXE (Run 3) and found a steep increase in success to 126 of the 295 cases (Fig. 1 ▶).

Bottom Line: AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, 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.

Show MeSH
Related in: MedlinePlus