User Tools

Site Tools


Epitope Assembly

Epitope Assembly is concerned with ordering epitopes into a string-of-beads poly-peptide which maximizes the probability that the epitopes will be fully recovered after proteasomal cleavage. This is an important step for vaccine design and has potentially high impact on the efficacy of the designed vaccine. Epitope Assembly formulates the epitope ordering problem as a traveling salesperson problem where epitopes represent the cities to visit and the distances between the cities represent the recovery probabilities.

The configuration steps of Epitope Assembly are explained in the following:

Step 1: Data Input

Epitope Assembly supports two types of input:

  1. Peptide list From History. Use this possibility to select a protein fasta file from the History panel.
  2. Peptide sequence(s). This input field provides the possibility to paste own peptide sequences. Start each peptide sequence in a new line.

Files can be uploaded with the (Figure 1 (1.)) Upload File tool or the (Figure 1 (2.)) jQuery Upload tool. Figure 1. Upload possibilities. 1. Upload tool. 2. jQuery Upload tool.

After execution, all peptide pairs are generated and the cleavage probabilities between the two peptides is predicted using proteasomal cleavage site prediction tools. Currently Epitope Assembly supports two proteasomal cleavage site prediction methods:

  1. PCM [1] is a position specific scoring matrix derived from degradation experiments of β-casein [2], enolase [3] and prion proteins [4].
  2. NetChop [5] is an artificial neural network trained on naturally processed HLA I epitopes. The authors argue that naturally processed HLA I epitopes represent the closest resource to in vivo cleavage data since the majority of HLA I epitopes underwent proteasomal degradation.

Peptide or protein sequences containing non-standard amino acids are not considered in epitope prediction.

Advanced Options

Proteasomal cleavage prediction is performed with PCM by default. If you want to change it to NetChop select Set advanced option values in the Advanced Options drop-down menu and select NetChop.

Additionally, you can specify whether unfavorable proteasom cleavage sites within epitopes induced by the ordering are punished (i.e. subtracted from the recovery probability). For doing so, choose Consider also cleavage sites within epitopes in the Advanced Cleavage Site Settings drop-down menu and state how strong cleavage sites within epitopes should influence the assembly by specifying a Weight [0,1].

Step 2: Result

Two outputs are generated. The first output is an internal representation of the assembly. The second output is an interactive html output of the assembly results.

Figure 2. Cleavage scores for each pair of epitopes.

It summarizes the configuration and shows the cleavage scores for each epitope pair in a table (Figure 2, the lower the better). Additionally, the output provides the finished string-of-beads poly-peptide oriented from N- to C-terminus (Figure 3).

Figure 3. Final string-of-beads design for ten epitopes.

You can download the cleavage prediction table by clicking Save and selecting either CSV or XLS as output format. By clicking Print, the table is completely extended to be able to use the Browser print function. To return to the normal view hit ESC.


  1. Donnes, P, and Kohlbacher, O. (2005). Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci, 14(8), 2132-2140. doi: 10.1110/ps.051352405
  2. Emmerich, N.P., Nussbaum, A.K., Stevanovicá, S., Priemer, M., Toes, R.E., Rammensee, H.-G., and Schild, H. (2000). The human 26 S and 20 S proteasomes generate overlapping but different sets of peptide fragments from a model protein substrate. J. Biol. Chem. 275 21140– 21148
  3. Nussbaum, A.K. (2001). “From the test tube to the World Wide Web.” Ph.D. thesis, Eberhard-Karls-Universitát, Tübingen, Germany.
  4. Tenzer, S., Stoltze, L., Schönfisch, B.,Dengjel, J., Müller, M., Stevanovicá, S., Rammensee, H.-G., and Schild, H. (2004). Quantitative analysis of prion-protein degradation by constitutive and immuno-20S proteasomes indicates differences correlated with disesase susceptibility. J. Immunol. 172 1083–1091.
  5. Nielsen, M, Lundegaard, C, Lund, O, and Kesmir, C. (2005). The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics, 57(1-2), 33-41. doi: 10.1007/s00251-005-0781-7
epitope_assembly.txt · Last modified: 2014/12/18 16:07 by schubert