RNA is a key regulator of almost every cellular process, and the structures adopted by RNA
molecules are thought to be central to their functions. The recent fast-paced evolution of high …

RNAs fold into 3D structures that range from simple helical elements to complex tertiary
structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory …

The nucleolus is the largest biomolecular condensate and facilitates transcription,
processing, and assembly of ribosomal RNA (rRNA). Although nucleolar function is thought …

Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an
atomic level of detail the conformational changes undergone by proteins. The application of …

The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence
and electrostatic parameters were determined from high-level quantum mechanical data …

RNA performs and regulates a diverse range of cellular processes, with new functional roles
being uncovered at a rapid pace. Interest is growing in how these functions are linked to …

RNA secondary structure plays essential roles in encoding RNA regulatory fate and function.
Most RNAs populate ensembles of alternatively paired states and are continually unfolded …

RNAs can begin to fold immediately as they emerge from RNA polymerase. During
cotranscriptional folding, interactions between nascent RNAs and ligands are able to direct …

RNA 3D structures are critical for understanding their functions. However, only a limited
number of RNA structures have been experimentally solved, so computational prediction …

The series of RNA folding events that occur during transcription can critically influence
cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a …