ArticleMolecules (Basel, Switzerland)2018
Exploring Protein Cavities through Rigidity Analysis.
Article in Molecules (Basel, Switzerland), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- In Silico Strategies for Characterizing Inner Cavities of Lipid-Binding Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors.Journal of chemical information and modeling · 2020Article
- Computational Structural Biology: Successes, Future Directions, and Challenges.Molecules (Basel, Switzerland) · 2019Review
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Authors and funding
3 authors.
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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.
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