This repository offers a series of Python scripts designed to analyze the three-dimensional structure of multiple RNA molecules.

--- 3D_RNAlysis is currently under development ---

• Base Pair Detection: The included scripts allow for the identification of single chain RNAs intra-bp, returning the type of interaction (Watson-Crick, Hogsteen, Sugar) using Biotite packages.
• Hydrogen Bond Identification: In addition to base pairs, the user is allowed to compute all H-bonds in a RNA structure for a more exhaustive analysis.
• RNA Superimposition: Given a multiple set of RNAs, 3D-RNAlysis can superpose the structures and compute RMSD and TM-score using US-align packages using two methods.
  • 1 vs 1: Every structure is superimposed with the rest of files in order to generate a matrix of RMSDs and TM-scores
  • All vs All: Given a multiple set of structures, a single superposition is given for all RNAs with a unique average RMSD.
• Analysis and Clustering:

If you encounter any problems or have any suggestions, please open an issue in this repository. We'll be happy to assist you.

Hi there! 👋 My name is Guillem Arasa and I'm currently pursuing a Master's degree in Atomistic and Multiscale Computational Modelling in Physics, Chemistry and Biochemistry at Universitat de Barcelona (UB) and Universitat Politècnica de Catalunya (UPC). This code is being developed by myself, Dr. Isaac Filella and PhD Júlia Vilalta at Barcelona Supercomputing Center.