Article
Received: 1 June 2008; Revised: 18 August 2008; Accepted: 21 August 2008
10.1002/pro.8 About DOI
RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation |
| Will Sheffler 1, David Baker 2 * |
| 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065 2Department of Biochemistry, University of Washington, Seattle, Washington 98195 |
| email: David Baker (dabaker@u.washington.edu) |
*Correspondence to David Baker, University of Washington, J 567 Health Sciences Bldg, Box 357350, Seattle, WA
Funded by:
Genome Training Grant and the Howard Hughes Medical Institute
| Keywords |
| protein structure/folding structure crystallography computational analysis of protein structure protein structure prediction hydrophobic interactions protein structures - new underpacking validation visualization |
| 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. |
Received: 1 June 2008; Revised: 18 August 2008; Accepted: 21 August 2008
| Digital Object Identifier (DOI) |
10.1002/pro.8 About DOI
