Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 11 (November 2013)

research papers

Acta Cryst. (2013). D69, 2194-2201    [ doi:10.1107/S0907444913018453 ]

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden

Abstract: AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

Keywords: molecular replacement; AMPLE; NMR structures; search models.

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[ doi:10.1107/S0907444913018453/kw5070sup1.pdf ]
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