In November 2023, our EXA4MIND consortium member Michal Otyepka (IT4Innovations), in collaboration with researchers from the Institute of Biophysics of the Czech Academy of Sciences and the Czech Advanced Technology and Research Institute, published a journal paper with the title ‘Simple Adjustment of Intra-nucleotide Base-phosphate Interaction in OL3 AMBER Force Field Improves RNA Simulations’.

Molecular dynamics (MD) simulation is an established theoretical tool that benefits from the ability to overcome experimental limits when finding links between RNA structure, dynamics, and function. This paper, which brings significant advancement in MD, demonstrates insights into RNA structural dynamics at atomistic description, essential for understanding biomolecular motions and processes.

More specifically, the paper suggests a correction for the widely used AMBER OL3 force field (ff) by simply adjusting nonbonded parameters. The scientists observed that structural ensembles of small RNA benchmark motifs simulated with the NBfix0BPh modification provide better agreement with experiments, and therefore suggest that the combination of OL3 RNA ff and NBfix0BPh modification is a viable option to improve RNA MD simulations. The paper is peer-reviewed and published through open access by the Journal of Chemical Theory and Computation. The supporting information containing details about standard MD simulations of various RNA and DNA motifs, supporting tables and figures to the article is also available free of charge via the Internet at http://pubs.acs.org/.

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