Recent advancements in small RNA sequencing have unveiled a previously hidden world of
regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small …

Foundational models of transcriptional regulation involve the assembly of protein complexes
at DNA elements associated with specific genes. These assemblies, which can include …

Knowing the 3D structures formed by the various conformations populating the RNA free-
energy landscape, their relative abundance, and kinetic interconversion rates is required to …

The rational targeting of RNA with small molecules is hampered by our still limited
understanding of RNA structural and dynamic properties. Most in silico tools for binding site …

RNAs are remarkably versatile molecules that can fold into intricate three-dimensional (3D)
structures to perform diverse cellular and viral functions. Despite their biological importance …

Much of the human genome is transcribed into RNAs, many of which contain structural
elements that are important for their function. Such RNA molecules—including those that are …

Computational RNA design tasks are often posed as inverse problems, where sequences
are designed based on adopting a single desired secondary structure without considering …

Determining the structure and mechanisms of all individual functional modules of cells at
high molecular detail has often been seen as equal to understanding how cells work …

Highlights•Conformational penalties to form alternative conformational states of nucleic
acids greatly contribute to nucleic acid-protein recognition.•Methods to determine nucleic …

Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities
of the conformations can be predictors of cell function. The conformational states that the …