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AlphaFold3 for RNA Folding

AlphaFold3 (aka AF3) is a newer version of AF2 using diffusion for predicting the 3D structure of proteins + nucleic acids + small molecules + post-translational modification. It is capable of multi-chains and therefore is also a cofolding or docking method.

AlphaFold3 Examples and Folding Scripts​

Inputs for Alphafold 3​

Protein sequence(s): A string of the single letter amino acid sequence.
RNA sequence(s): A string of the RNA sequence.
DNA sequence(s): A string of the DNA sequence.
Small molecule SMILE(s): A string representing a small molecule.

Outputs for Alphafold 3​

PDB file: File containing the predicted 3D coordinates of each atom in the input.
pLDDT: Specified in the b-factor column of the PDB file. A per residue confidence score between 0 and 100 with higher being better.

Evaluate RNA Structure Predictions​

  • pLDDT: Predicted local distance difference test (pLDDT) is a per residue confidence score. 0-50: very low (correlated with disorder/flexibility), 50-70: low, 70-90: high, 90-100: very high (highly structured/stable).
  • PAE: Predicted aligned error (PAE) is a residue pair confidence. 0-5 angstroms (low): The relative position between the 2 residues is known (they move together). 20+ anstroms (high): The relative position is not known (they move independently of each other)