In addition to messenger RNA (mRNA) that provide the code for proteins, there are other RNAs that exert their function just as RNA, usually referred to as non-coding […]

Structural RNAs exhibit a vast array of recurrent short three-dimensional (3D) elements found in loop regions involving non-Watson–Crick interactions that help arrange canonical double helices into tertiary structures. Here we present CaCoFold-R3D, a probabilistic grammar that predicts these RNA 3D motifs (also termed modules) jointly with RNA secondary structure over a sequence or alignment. CaCoFold-R3D uses evolutionary information present in an RNA alignment to reliably identify canonical helices (including pseudoknots) by covariation. Here we further introduce the R3D grammars, which also exploit helix covariation that constrains the positioning of the mostly noncovarying RNA 3D motifs. Our method runs predictions over an almost-exhaustive list of over 50 known RNA motifs (‘everything’). Motifs can appear in any nonhelical loop region (including three-way, four-way and higher junctions) (‘everywhere’). All structural motifs as well as the canonical helices are arranged into one single structure predicted by one single joint probabilistic grammar (‘all-at-once’). Our results demonstrate that CaCoFold-R3D is a valid alternative for predicting the all-residue interactions present in a RNA 3D structure. CaCoFold-R3D is fast and easily customizable for novel motif discovery and shows promising value both as a strong input for deep learning approaches to all-atom structure prediction as well as toward guiding RNA design as drug targets for therapeutic small molecules.

President Donald Trump told reporters on Tuesday in the Oval Office that the White House had “reached a deal” with Harvard, before cautioning that the agreement had not been finalized.

Our oldest educational institution is standing up to the Trump onslaught. We can't know how this will end. But we can note the different narratives that different news organizations are presenting.

Moving beyond the simplistic view of mitochondria as the power house of the cell, Roger et al. present the immense diversity of mitochondria and mitochondrial functions across eukaryotes, and bring th...

Trump underlined his financial goal in comments to Education Secretary Linda McMahon at a cabinet meeting on Tuesday, days before classes start at Harvard.

Demand RFK Jr. Resign: Petition for a Healthy America