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Molecules 2018, 23(2), 351; https://doi.org/10.3390/molecules23020351

Exploring Protein Cavities through Rigidity Analysis

1
Department of Computer Science, Western Washington University, 516 High Street, Bellingham, WA 98225, USA
2
Department of Computer Science and Engineering, Lehigh University, 19 Memorial Drive West, Bethlehem, PA 18015, USA
*
Author to whom correspondence should be addressed.
Received: 23 December 2017 / Revised: 25 January 2018 / Accepted: 31 January 2018 / Published: 7 February 2018
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Abstract

The geometry of cavities in the surfaces of proteins facilitates a variety of biochemical functions. To better understand the biochemical nature of protein cavities, the shape, size, chemical properties, and evolutionary nature of functional and nonfunctional surface cavities have been exhaustively surveyed in protein structures. The rigidity of surface cavities, however, is not immediately available as a characteristic of structure data, and is thus more difficult to examine. Using rigidity analysis for assessing and analyzing molecular rigidity, this paper performs the first survey of the relationships between cavity properties, such as size and residue content, and how they correspond to cavity rigidity. Our survey measured a variety of rigidity metrics on 120,323 cavities from 12,785 sequentially non-redundant protein chains. We used VASP-E, a volume-based algorithm for analyzing cavity geometry. Our results suggest that rigidity properties of protein cavities are dependent on cavity surface area. View Full-Text
Keywords: protein; cavity; rigidity analysis protein; cavity; rigidity analysis
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Mason, S.; Chen, B.Y.; Jagodzinski, F. Exploring Protein Cavities through Rigidity Analysis. Molecules 2018, 23, 351.

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