Journal
PROTEIN SCIENCE
Volume 18, Issue 1, Pages 229-239Publisher
WILEY
DOI: 10.1002/pro.8
Keywords
protein structure/folding; structure; crystallography; computational analysis of protein structure; protein structure prediction; hydrophobic interactions; protein structures-new underpacking; validation; visualization
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Funding
- Genome Training Grant
- Howard Hughes Medical Institute
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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.
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