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AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models

Acta Cryst. (2012). D68, 1622-1631 (

[Snapshots] Snapshots along structure solution by AMPLE. A cluster of ab initio models is generated by structural alignment (top). Multiple truncated ensembles (e.g. lower left) are derived from it, varying in their treatment, and trialled by MR. A successful solution and rebuild are compared to the final structure lower right.

Ab initio protein structure prediction, by programs such as Rosetta, can provide starting models for solving novel structures from crystallographic data. Rather than trying to construct the single best model, we generate ensembles which are known to work well in molecular replacement (MR). We have demonstrated the feasibility of an approach based on identification and extraction of incomplete but locally accurate search models from rapidly obtained ab initio predictions. 43% of a set of small (<120 residues) proteins were successfully solved.

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