Efficient Prediction Model of mRNA End-to-End Distance and Conformation: Three-Dimensional RNA Illustration Program (TRIP).

The secondary and tertiary structures of RNA play a vital role in the regulation of biological reactions. These structures have been experimentally studied through in vivo and in vitro analyses, and in silico models have become increasingly accurate in predicting them. Recent technologies have diversified RNA structure predictions, from the earliest thermodynamic and molecular dynamic-based RNA structure predictions to deep learning-based conformation predictions in the past decade. While most research on RNA structure prediction has focused on short non-coding RNAs, there has been limited research on predicting the conformation of longer mRNAs. Our study introduces a computer simulation model called the Three-dimensional RNA Illustration Program (TRIP). TRIP is based on single-chain models and angle restriction of each bead component from previously reported single-molecule fluorescence in situ hybridization (smFISH) experiments. TRIP is a fast and efficient application that only requires up to three inputs to acquire outputs. It can also provide a rough visualization of the 3D conformation of RNA, making it a valuable tool for predicting RNA end-to-end distance.