ArticleMolecular physics2019
REDAN: Relative Entropy-Based Dynamical Allosteric Network Model.
Article in Molecular physics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Functional dynamics of water in New Delhi metallo-β-lactamase catalysis.Protein science : a publication of the Protein Society · 2026Article
- Machine learning and protein allostery.Trends in biochemical sciences · 2023Review
- Allosteric regulation in STAT3 interdomains is mediated by a rigid core: SH2 domain regulation by CCD in D170A variant.PLoS computational biology · 2022Article
- Allosteric control of ACE2 peptidase domain dynamics.Organic & biomolecular chemistry · 2022Article
- SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations.PloS one · 2022Article
- Deciphering the Allosteric Process of theThe journal of physical chemistry. B · 2020Article
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- Directed kinetic transition network model.The Journal of chemical physics · 2019Article
- Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis.PLoS computational biology · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Protein allostery is ubiquitous phenomena that are important for cellular signaling processes. Despite extensive methodology development, a quantitative model is still needed to accurately measure protein allosteric response upon external perturbation. Here, we introduced the relative entropy concept from information theory as a quantitative metric to develop a method for measurement of the population shift with regard to protein structure during allosteric transition. This method is referred to as relative entropy-based dynamical allosteric network (REDAN) model. Using this method, protein allostery could be evaluated at three mutually dependent structural levels: allosteric residues, allosteric pathways, and allosteric communities. All three levels are carried out using rigorous searching algorithms based on relative entropy. Application of the REDAN model on the second PDZ domain (PDZ2) in the human PTP1E protein provided metric-based insight into its allostery upon peptide binding.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.