The local topological free energy of proteins

DOI10.1101/2021.01.06.425494MaRDI QIDQ2235495zbMATH OpenOpenAlexFDO

Authors Quenisha Baldwin, Eleni Panagiotou

Publication date 21 October 2021

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Copyright license Creative Commons Attribution-NoDerivs 4.0 International

Full work available at URL https://doi.org/10.1101/2021.01.06.425494

zbMATH Keywords

protein foldingprotein structuretopologytorsionwrithe

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

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Cites work

• A topological characterization of knots and links arising from site-specific recombination
• A topological study of protein folding kinetics
• Exploring the correlation between the folding rates of proteins and the entanglement of their native states
• scientific article; zbMATH DE number 3565702 (Why is no real title available?)
• Knot polynomials of open and closed curves
• Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases
• Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex
• The effects of density on the topological structure of the mitochondrial DNA from trypanosomes
• The linking number and the writhe of uniform random walks and polygons in confined spaces
• The mean squared writhe of alternating random knot diagrams
• Topological descriptions of protein folding
• Untangling DNA

Cited in

(9)

• Understanding the role of the topology in protein folding by computational inverse folding experiments
• Geometry, thermodynamics, and protein
• Global and local prediction of protein folding rates based on sequence autocorrelation information
• Folding degrees of azurins and pseudoazurins: Implications for structure and function
• A localized protein-folding problem
• A topological study of protein folding kinetics
• THE STRUCTURE OF THE FREE ENERGY SURFACE OF COARSE-GRAINED OFF-LATTICE PROTEIN MODELS
• Study of the relation between the protein folding rate and its topological structure
• Funnels in energy landscapes

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