Building RNA Backbone in Constant Time by Numerical Approximation
Thibault, P.; Major, F.
Show abstract
We present a numerical approximation method designed to swiftly create RNA ribose conformations in constant time. The methods parameterization relies on the atomic coordinates of a given base along with its two neighboring phosphate groups. Such a parameterization suits three dimensional modeling engines that determine the RNA conformational search space using base operations instead of backbone sampling. These engines consider phosphate groups as part of the base rigid bodies. Reconstructing ribose conformations result in less than 1 [A] of RMSD (root-mean-square deviation) compared to original conformations derived from high-resolution X-ray crystallographic structures. By incorporating this ribose construction method into MC-Sym, a well-established RNA three dimensional modeling software, we streamline the modeling process into two phases. This enhances the search algorithms speed and improves model consistency and precision. Additionally, we employed the method to pinpoint 27 irregular ribose stereoisomers in high-resolution RNA X-ray crystal structures.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- A Comprehensive Survey on the Nature of Ring:Ring Nucleobase Stacking Interactions in RNA: Occurrence, Structural Variability and Classification of the Associated Contacts 95%
- Influence of stereochemistry in a local approach for calculating protein conformations 94%
- Optimizing On-the-Fly Probability Enhanced Sampling for Complex RNA Systems: Sampling Free Energy Surfaces of an H-Type Pseudoknot 94%
Similar papers in this journal
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.