Additive CHARMM force field for naturally occurring modified ribonucleotides - École polytechnique Accéder directement au contenu
Article Dans Une Revue Journal of Computational Chemistry Année : 2016

Additive CHARMM force field for naturally occurring modified ribonucleotides

Résumé

More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. (C) 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Fichier principal
Vignette du fichier
Xu_et_al-2016-Journal_of_Computational_Chemistry.pdf (1.19 Mo) Télécharger le fichier
Origine : Publication financée par une institution
Loading...

Dates et versions

hal-01315145 , version 1 (18-05-2016)

Identifiants

Citer

You Xu, Kenno Vanommeslaeghe, Alexey Aleksandrov, Alexander D. Mackerell, Lennart Nilsson. Additive CHARMM force field for naturally occurring modified ribonucleotides. Journal of Computational Chemistry, 2016, 37 (10), pp.896-912. ⟨10.1002/jcc.24307⟩. ⟨hal-01315145⟩
247 Consultations
540 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More