Circuit Topology Approach for the Comparative Analysis of Intrinsically Disordered Proteins

Barbara Scalvini, Vahid Sheikhhassani, Nadine van de Brug, Laurens W. H. J. Heling, Jeremy D. Schmit, Alireza Mashaghi

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


Intrinsically disordered proteins (IDPs) lack a stable native conformation, making it challenging to characterize their structure and dynamics. Key topological motifs with fundamental biological relevance are often hidden in the conformational noise, eluding detection. Here, we develop a circuit topology toolbox to extract conformational patterns, critical contacts, and timescales from simulated dynamics of intrinsically disordered proteins. We follow the dynamics of IDPs by providing a smart low-dimensionality representation of their three-dimensional (3D) configuration in the topology space. Such an approach allows us to quantify topological similarity in dynamic systems, therefore providing a pipeline for structural comparison of IDPs.
Original languageEnglish
Pages (from-to)2586-2602
Number of pages17
JournalJournal of Chemical Information and Modeling
Issue number8
Publication statusPublished - 24 Apr 2023


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