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Article

Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics.

Journal of computer-aided molecular design - 21 Apr 2025

Pandit Akansha, Srivastava Shubham, Kumar Neeraj, Sawant Devesh M

Abstract excerpt

Programmed ribosomal frameshifting in Simian retrovirus-1 (SRV-1) is sensitive to the mechanical properties of an RNA pseudoknot. Unravelling these mechanical intricacies via unfolding reveals fundamental insights into their structural dynamics. Using constant velocity steered molecular dynamics (CV-SMD) simulations, we explored the unfolding dynamics and the impact of mutations on the unfolding pathway of the...

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Methodology Data sources Editorial policy Privacy Delete account & data About Contact Helena Bioinformatics

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Identifiers

PMID: 40259108
DOI: 10.1007/s10822-025-00598-0

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