Welcome to SYFPEITHI 2

The SYFPEITHI-Server has been completely reprogrammed: Results are delivered much faster and new features (described below) have been added.

Find your ligand or epitope

Compiled from published reports only SYFPEITHI's "Find your ligand or epitope" comprises 6793 peptide sequences known to bind class I and class II MHC molecules.
NEW: We have added links to UniProt Database. Click here for more information on how UniProt-Links have been validated. Links to the ENA Sequence Database(EMBL-Bank) are still available.
NEW: The molecular Masses of all peptide sequences are now calculated from its constituens aa. Click here to find out more.

Epitope Prediction

NEW: 100 prediction matrices have been added and two have been updated.
NEW: Prediction scores are now given in per cent relative to the maximum score available for a given MHC-type and aminoacid frame length.
NEW: You might now filter your results by a minimum score, thus ignoring all results with scores below a certain treshold.
IMPROVED: Results are now delivered up to 100 times faster than with previous SYFPEITHI. Even with long sequences (2048 amino acids) and three MHC-types selected, the results will appear within seconds.

Information

Here you will find updated additional Information and References

Links to external Protein and Sequence Resources

SYFPEITHI Version 2.x still provides external reference to the ENA Sequence Database (formerly known as EMBL-Bank) of the European Bioinformatics Institute (EMBL-EBI) for its peptide sources with ENA-Links.

Additionally we now also provide links to UniProt's protein database via the UniProt Knowledge Base Accession Number (UniProtKB AC). Almost all ENA-Sequence-IDs could be mapped to UniProtKB ACs. These mappings have been validated in a semi-automated way. The six validation-levels resulting from this process are given in the following table:

Link to UniProt.org	Description
UPposM (r)	UPposM (u)	The sequence of SYFPEITHI-Ligand or T-cell epitope has a match in UniProt's protein-sequence.
UPseqM (r)	UPseqM (u)	The sequence of SYFPEITHI-Ligand or T-cell epitope matches UniProt's protein-sequence, but position of the matches differ.
UPnoM (r)	UPnoM (u)	Sequence of SYFPEITHI-Ligand or T-cell epitope has no match in the corresponding UniProt.org protein-sequence.

Link to UniProt.org

Description

show protein(s) in UniProt's UniProtKB database

show protein(s) in UniProt's UniParc database

In UniProt's future Release 2026 02 some protein entries will be removed from UniProtKB database, but stay accessible in UniParc database. In SYFPEITHI reviewed Links are marked with (r) as opposed to unreviewed Links marked (u).

UPposM (r)

UPposM (u)

The sequence of SYFPEITHI-Ligand or T-cell epitope has a match in UniProt's protein-sequence.

UPseqM (r)

UPseqM (u)

The sequence of SYFPEITHI-Ligand or T-cell epitope matches UniProt's protein-sequence, but position of the matches differ.

UPnoM (r)

UPnoM (u)

Sequence of SYFPEITHI-Ligand or T-cell epitope has no match in the corresponding UniProt.org protein-sequence.

Note that for a few SYFPEITHI-proteins the ENA-Sequence-ID could not be mapped to a UniProtKB AC. In this case, a lookUP-link offers to lookup the protein name on UniProt.org. You might edit the search string in UniProt and compare the results found there to the contents of the ENA-Link.

Molecular mass of Ligands and epitopes

For each ligand or epitope peptide the calculated molecular mass (mm) in dalton is given.

The calculation consists in adding up the average residue masses of the peptide's constituent amino acids plus the masses of the N-terminus (H-) and C-Terminins (OH-) according to this reference.