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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.

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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
Chain lengths and secondary-structure classes of targets uniquely solved using either QUARK-derived (Run 1) or ROSETTA-derived search models (18 and 42 cases, respectively; Bibby et al., 2012 ▶).
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fig4: Chain lengths and secondary-structure classes of targets uniquely solved using either QUARK-derived (Run 1) or ROSETTA-derived search models (18 and 42 cases, respectively; Bibby et al., 2012 ▶).

Mentions: The search models from QUARK predictions performed similarly across secondary-structure classes as the ROSETTA-derived search models (Fig. 4 ▶). In our test set there are 77 all-α, 44 all-β and 174 αβ targets. Particularly noticeable is the poor performance of both programs with all-β targets. The two all-β targets previously solved were also solved by a QUARK-derived search model, but no further successes were added. In contrast, 60 all-α targets solved previously with Phaser (Bibby et al., 2012 ▶) were complemented by four additional successes from QUARK (Run 1), taking the success rate between the two runs to 83%. Remarkably, including Run 3, with modern versions of Phaser and SHELXE, adds a further seven targets solved at least once between Runs 1 and 3 here and previous results (Bibby et al., 2012 ▶): thus, very nearly all of the all-α targets in the set (92%) were solved at least once. In the αβ class, it is notable how the complementarity with QUARK is focused in the larger target-size range above 100 residues or so. As previously (Bibby et al., 2012 ▶), success close to the upper size limit should encourage the application of AMPLE to larger targets.


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)

Chain lengths and secondary-structure classes of targets uniquely solved using either QUARK-derived (Run 1) or ROSETTA-derived search models (18 and 42 cases, respectively; Bibby et al., 2012 ▶).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Chain lengths and secondary-structure classes of targets uniquely solved using either QUARK-derived (Run 1) or ROSETTA-derived search models (18 and 42 cases, respectively; Bibby et al., 2012 ▶).
Mentions: The search models from QUARK predictions performed similarly across secondary-structure classes as the ROSETTA-derived search models (Fig. 4 ▶). In our test set there are 77 all-α, 44 all-β and 174 αβ targets. Particularly noticeable is the poor performance of both programs with all-β targets. The two all-β targets previously solved were also solved by a QUARK-derived search model, but no further successes were added. In contrast, 60 all-α targets solved previously with Phaser (Bibby et al., 2012 ▶) were complemented by four additional successes from QUARK (Run 1), taking the success rate between the two runs to 83%. Remarkably, including Run 3, with modern versions of Phaser and SHELXE, adds a further seven targets solved at least once between Runs 1 and 3 here and previous results (Bibby et al., 2012 ▶): thus, very nearly all of the all-α targets in the set (92%) were solved at least once. In the αβ class, it is notable how the complementarity with QUARK is focused in the larger target-size range above 100 residues or so. As previously (Bibby et al., 2012 ▶), success close to the upper size limit should encourage the application of AMPLE to larger targets.

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