{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T06:16:08Z","timestamp":1769753768212,"version":"3.49.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,2,11]],"date-time":"2024-02-11T00:00:00Z","timestamp":1707609600000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Scientific and Technological Research Council of Turkey","award":["119F392"],"award-info":[{"award-number":["119F392"]}]},{"name":"NATO Science for Peace Program","award":["G5685"],"award-info":[{"award-number":["G5685"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Proteins are dynamic entities that undergo conformational changes critical for their functions. Understanding the communication pathways and information transfer within proteins is crucial for elucidating allosteric interactions in their mechanisms. This study utilizes mutual information (MI) analysis to probe dynamic allostery. Using two cases, Ubiquitin and PLpro, we have evaluated the accuracy and limitations of different approximations including the exact anisotropic and isotropic models, multivariate Gaussian model, isotropic Gaussian model, and the Gaussian Network Model (GNM) in revealing allosteric interactions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our findings emphasize the required trajectory length for capturing accurate mutual information profiles. Long molecular dynamics trajectories, 1\u2009ms for Ubiquitin and 100 \u00b5s for PLpro are used as benchmarks, assuming they represent the ground truth. Trajectory lengths of approximately 5 \u00b5s for Ubiquitin and 1 \u00b5s for PLpro marked the onset of convergence, while the multivariate Gaussian model accurately captured mutual information with trajectories of 5\u2009ns for Ubiquitin and 350\u2009ns for PLpro. However, the isotropic Gaussian model is less successful in representing the anisotropic nature of protein dynamics, particularly in the case of PLpro, highlighting its limitations. The GNM, however, provides reasonable approximations of long-range information exchange as a minimalist network model based on a single crystal structure. Overall, the optimum trajectory lengths for effective Gaussian approximations of long-time dynamic behavior depend on the inherent dynamics within the protein's topology. The GNM, by showcasing dynamics across relatively diverse time scales, can be used either as a standalone method or to gauge the adequacy of MD simulation lengths.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Mutual information codes are available at https:\/\/github.com\/kemaldemirtas\/prc-MI.git.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae076","type":"journal-article","created":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T21:07:49Z","timestamp":1707426469000},"source":"Crossref","is-referenced-by-count":16,"title":["Dynamic correlations: exact and approximate methods for mutual information"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-1420-1813","authenticated-orcid":false,"given":"Kemal","family":"Demirta\u015f","sequence":"first","affiliation":[{"name":"Department of Chemical 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