Create a biomolecule based on an experimental crystal structure:

Now take the peptide sequence from that biomolecule and fold it:

The predicted structure's 3D coordinates are unrelated to the experimental structure:

Now align the predicted structure with the experimental structure and show them in 3D:

View the sequence alignment:

Find the RMSD error in the alignment:

Align a smaller peptide to a specific chain in a larger peptide:

Align the smaller peptide to a different chain:

BioMoleculeAlign can align peptides with dissimilar sequences but similar 3D structures:

The structures are aligned very well as shown by the low RMSD error and high TM-score:

Nearly all the amino acid residues participate in the alignment:

But there are significant differences in the two sequences:

Align an RNA strand to the RNA portion of an RNA-peptide complex:

Compare the structures of Cyclin-dependent kinase 2 from two different organisms from AlphaFold Database:

Align two large biomolecular assemblies: