Year: 2012
Type: preprint
Abstract: We exploit recent advances in computational topology to study the compressibility of various pro-teins found in the Protein Data Bank (PDB). Our fundamental tool is the persistence diagram, a topological invariant which captures the sizes and robustness of geometric features such as tunnels and cavities in protein molecules. Based on certain physical and chemical properties conjectured to impact protein compressibility, we propose a topological measurement CP for each protein molecule P. CP can be efficiently computed from the PDB data of P. Our main result establishes a clear linear correlation between CP and the experimentally measured compressibility of most proteins for which both PDB information and experimental compressibility data are available.
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
Awards: G1389074705, CDI-Type II: Collaborative Research: Computational Homology, Jamming, and Force Chains in Dense Granular Flows, G2581719517, Collaborative proposal: Computing Dynamics of Multiparameter Systems, CDI-TYPE II--COLLABORATIVE RESEARCH: Using Algebraic Topology to Connect Models with Measurements in Complex Nonequilibrium Systems
OpenAlex ID: W2253971223