Reparameterizations of the χ Torsion and Lennard‐Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines

摘要: UNLABELLED The currently available force field parameters for modified RNA residues in AMBER show significant deviations conformational properties from experimental observations. examination of the transferability recently revised torsion revealed that there was an overall improvement some modifications but improvements were still insufficient describing sugar pucker preferences (J. Chem. Inf. MODEL 2014, 54, 1129-1142). Here, we report approach development and fine tuning 2-thiouridine, 4-thiouridine, pseudouridine with diverse preferences. χ reparameterized at individual nucleoside level. effect combining γ parameter modifying Lennard-Jones σ also tested by directly comparing obtained our extensive molecular dynamics simulations those © 2016 Wiley Periodicals, Inc.