Predicting the 3D structure of RNA is a significant challenge despite ongoing advancements
in the field. Although AlphaFold has successfully addressed this problem for proteins, RNA …

The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is
crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most …

A new computer program to annotate DNA and RNA three-dimensional structures, MC-
Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate …

To benchmark progress made in RNA three-dimensional modeling and assess newly
developed techniques, reliable and meaningful comparison metrics and associated tools …

Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied
using the ab initio quantum-chemical method with inclusion of electron correlation. The …

Three groups of molecular clusters were studied using the coupled cluster method with non-
iterative triple excitations (CCSD (T)) and the second-order Møller-Plesset perturbational …

Background Biotite is a program library for sequence and structural bioinformatics written for
the Python programming language. It implements widely used computational methods into a …

RNA modulation via small molecules is a novel approach in pharmacotherapies, where the
determination of the structural properties of RNA motifs is considered a promising way to …

The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–
quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high …

The hypothesis that RNA coaxial stacking can be predicted by free energy minimization
using nearest-neighbor parameters is tested. The results show 58.2% positive predictive …