Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent

Accurate modeling of the structural dynamics of ribonucleic acid (RNA) molecules, including common stem-loop motifs, remains challenging. This study presents <i>de novo</i> folding simulations of a diverse set of 26 RNA stem-loops, ranging from 10 to 36 residues, with and without bulges...

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Bibliographic Details
Main Author:	Tadashi Ando (673133) (author)
Published:	2025
Subjects:	Biophysics Biochemistry Molecular Biology Developmental Biology Cancer Infectious Diseases Computational Biology Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified Information Systems not elsewhere classified remaining duplex stems native base pairs implicit solvent model e1346 − e1355 de novo </ atomistic force field 9 – 4 8 – 8 3714 − 3728 including common stem approximately 4 å molecular dynamics simulations experimentally determined structures loop motifs represents loops containing bulges 26 rna stem rna structural dynamics loop folding using rna stem folding loops without bulges without bulges structural dynamics folding simulations loop motifs simulations using rna stem loop regions internal loop stem regions fundamental stem eight stem 18 stem 5 å 3 å internal loops hairpin loops values relative theory comput study presents simmerling group shaw group ribonucleic acid respective structures remains challenging extended conformations diverse set accurate modeling 5b00271 ). 36 residues
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Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent

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