Evolutionary information is central in Structural Bioinformatics through the use of Multiple Sequence Alignments (MSA).
While protein structure files (PDB) reference amino acids by their 3-letter name (which allow the specifications of a wide range of non-standard amino acids), sequence databases generally uses the 1-letter name and consider only the 20 standard proteogenic amino acids.
To simplify the 'translation' from protein structure to protein sequence, here is a mapping of 741 non-standard amino acids to their corresponding 'closest' standard amino acid (3-letter name).
Non standard amino acids list was found by scanning the SEQRES lines in 199.374 PDB structures from the RCSB: Protein Data Bank.
The corresponding standard amino acid was assigned using the 'Chemical Components in the PDB' database.
Only entries which Polymer type property is Amino Acid and which Standard parent property corresponds to one of the 20 standard proteogenic amino acids were kept.
The scanning was made on 15/05/2023.
GPL-3 or later.
Matsvei Tsishyn, Université Libre de Bruxelles, 3BIO-BioInfo: Computational Biology and Bioinformatics.