Project: Analysing AlphaFold3 for RNA structure prediction

The aim of this project was to investigate how well AlphaFold3 can predict the structure of RNAs that were not part of the AlphaFold3 training set. To do this, I focused on analyzing the RMSD, RMSD per residue, and structural motifs of the RNA structure predictions of a test set of new RNA structures deposited on PDB databank since 2023.

alphafold_structures

Directory contains all structure predictions made with AlphaFold3 for different datasets and additionally the pdb files from the experimental structure deposited on PDB.

analysis

Analysis directory contains all .ipynb evaluation files.

data_22

Output from NucleoSeeker for all RNA structures before 2022 from PDB.

data_23_24

Output from NucleoSeeker for all RNA structures from 2023 until October 2024 from PDB.

rna_only_23_24

Similar to data_23_24 but with additional filtering for RNA only. This directory contains only RNA that is deposited as isolated RNA structure in PDB.