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Protein Sci. 2009 Jan;18(1):229-39. doi: 10.1002/pro.8.

RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation.

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  • 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065, USA.

Abstract

We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures.

PMID:
19177366
[PubMed - indexed for MEDLINE]
PMCID:
PMC2708028
Free PMC Article

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