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Investigating Rigidity Properties of Protein Cavities

Published: 20 August 2017 Publication History

Abstract

Cavities in proteins facilitate a variety of biochemical processes. The shapes and sizes of cavities are factors that contribute to specificity in ligand binding, and docking with other biomolecules. A deep understanding of cavity properties may enable new insights into protein-protein interactions, ligand binding, and structure-based drug design studies. In this work we explore how biological properties such as size and residue membership of protein cavities correlate with the flexibility of the cavity as computed using an efficient graph theoretic rigidity algorithm. We hypothesize that various rigidity properties of protein cavities are dependent on cavity surface area. In this work we enumerate a set of cavity rigidity metrics, and demonstrate their use in characterizing over 120,000 cavities from approximately 2,500 chains. We show that cavity size indeed does correlate with some -- but not all -- cavity rigidity metrics.

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      cover image ACM Conferences
      ACM-BCB '17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics
      August 2017
      800 pages
      ISBN:9781450347228
      DOI:10.1145/3107411
      Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected].

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      Published: 20 August 2017

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      Author Tags

      1. cavity
      2. protein
      3. rigidity

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