Fatgraph models of proteins

DOI10.1002/CPA.20340MaRDI QIDQ3588800zbMATH OpenOpenAlexFDO

Authors Michael Knudsen, Carsten Wiuf, J. E. Andersen, Robert Penner

Publication date 10 September 2010

Published in Communications on Pure and Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0902.1025

Mathematics Subject Classification ID

Applications of graph theory (05C90) Computing methodologies and applications (68U99) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40)

Abstract: We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be stored and manipulated as triples of permutations, and these methods are therefore amenable to fast computer implementation. Applications include the refinement of structural protein classifications and the prediction of geometric and other properties of proteins from their chemical structures.

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Cites work

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Cited in

(17)

• The block spectrum of RNA pseudoknot structures
• On RNA-RNA interaction structures of fixed topological genus
• Statistics of topological RNA structures
• A topological framework for signed permutations
• Generation of RNA pseudoknot structures with topological genus filtration
• Skeletal configurations of ribbon trees
• Moduli spaces and macromolecules
• Computation and visualization of protein topology graphs including ligand information
• Topological language for RNA
• Topological classification and enumeration of RNA structures by genus
• scientific article; zbMATH DE number 1341919 (Why is no real title available?)
• scientific article; zbMATH DE number 861322 (Why is no real title available?)
• Fatgraph models of RNA structure
• Protein structures
• Knot theory in understanding proteins
• Shapes of topological RNA structures
• Enumeration of chord diagrams on many intervals and their non-orientable analogs

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