Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and <i>N</i>1-methylpseudouridine within RNA duplexes-Reference-Cited by-同舟云学术

Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N1-methylpseudouridine within RNA duplexes

Published:2024 Issue:2 Volume:26 Page:992-999
ISSN:1463-9076
Container-title:Physical Chemistry Chemical Physics
language:en
Short-container-title:Phys. Chem. Chem. Phys.

Author:

Dutta Nivedita¹^ORCID,Sarzynska Joanna²^ORCID,Deb Indrajit¹^ORCID,Lahiri Ansuman¹^ORCID

Affiliation:

1. Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India

2. Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland

Abstract

In this study, we propose a protocol for deriving nearest neighbor (NN) free energy parameters for pseudouridine and N1-methylpseudouridine from MD simulations using the linear interaction energy (LIE) approach.

Funder

Department of Science and Technology, Ministry of Science and Technology, India

Publisher

Royal Society of Chemistry (RSC)

Subject

Physical and Theoretical Chemistry,General Physics and Astronomy

Link

http://pubs.rsc.org/en/content/articlepdf/2024/CP/D3CP02442C

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