RosettaHoles2: a volumetric packing measure for protein structure refinement and validation

TitleRosettaHoles2: a volumetric packing measure for protein structure refinement and validation
Publication TypeJournal Article
Year of Publication2010
AuthorsSheffler, W., & Baker D.
JournalProtein science
Volume19
Issue10
Pagination1991-5
Date Published2010 Oct
ISSN1469-896X
KeywordsPrimary Publication
Abstract

We present an improved version of RosettaHoles, a methodology for quantitative and visual characterization of protein core packing. RosettaHoles2 features a packing measure more rapidly computable, accurate and physically transparent, as well as a new validation score intended for structures submitted to the Protein Data Bank. The differential packing measure is parameterized to maximize the gap between computationally generated and experimentally determined X-ray structures, and can be used in refinement of protein structure models. The parameters of the model provide insight into components missing in current force fields, and the validation score gives an upper bound on the X-ray resolution of Protein Data Bank structures; a crystal structure should have a validation score as good as or better than its resolution.

Alternate JournalProtein Sci.
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