antigenic

Function

Description

Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. This method is based on a single parameter and thus very simple to use.

Algorithm

Analysis of data from experimentally determined antigenic sites on proteins has revealed that the hydrophobic residues Cys, Leu and Val, if they occur on the surface of a protein, are more likely to be a part of antigenic sites. The method of Kolaskar and Tongaonkar to predict antigenic determinants in proteins is semi-empirical and makes use of physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes.

Usage

Command line arguments

Input file format

The input sequence can be one or more protein sequences.

Output file format

By default antigenic writes a 'motif' report file.

Data files

Antigenic uses a data file called Eantigenic.dat.

Here is the default Eantigenic.dat file: 

# Kolaskar AS and Tongaonkar PC (1990) FEBS Letters 276:172-174
# "A semi-emipirical method for prediction of antigenic determinants
# on protein antigens"
#
# TABLE 1: Occurrence of amino acids in epitopes, proteins and on the surface,
#         and their antigenic propensity, A(p), values
#
# 169 antigenic determinants experimentally determined. Selected those 156
# which have less than 20 amino acids per determinant (total 2066 residues).
# Calculated f(Ag) as frequency of occurrence of each residue in antigenic
# determinants [f(Ag) = Epitope_occurrence/2066].
#
# Used Hydrophilicity, Accessibility and Flexibility of Parker JMR, Guo D,
# Hodges, RS (1986) Biochemistry 25:5425-5432. In a given protein, calculated
# average for each 7-mer and assigned values to central residue of 7-mer.
# Residue considered to be on the surface if any of the 7-mer values was above
# the average for the protein. Used these results to get f(s) frequency of
# occurrence of amino acids at the surface.
#
# Original table covers the 20 naturally occurring amino acids.
# Values for B, Z, X use weighted averages from Edayhoff.dat
# and are ignored when calculating totals
#
# Antigenic propensity column A(p) = f(Ag)/f(s)
#
# f(s) values below were back-calculated from the table in the paper
#
# Prediction algorithm:
#
# 1. calculate average propensity  for each overlapping 7-mer, assign to
#    central residue (i+3)
#
# 2. calculate average for whole protein A(p)av
#
# 3. (a) if average for whole protein >= 1.0 then all residues having
#         >= 1.0 are potentially antigenic.
#    (b) if average for whole protein <  1.0 then all residues having
#         > average for whole protein (??? paper has a mangled
#        formula here :-) are potentially antigenic.
#
# 4. Find 6-mers where all residues are selected by step 3 above
#
#                                               Antigenic  Surface  Antigenic
# Amino     -- Occurrence of amino acids in --   frequency frequency propensity
# Acid       Epitopes      Surface     Protein   f(Ag)    f(s)      A(p)
  A             135          328         524     0.065    0.061     1.064
  B             107          334         410     0.052    0.062     0.827
  C              53           97         186     0.026    0.018     1.412
  D             118          352         414     0.057    0.066     0.866
  E             132          401         499     0.064    0.075     0.851
  F              76          180         365     0.037    0.034     1.091
  G             116          343         487     0.056    0.064     0.874
  H              59          138         191     0.029    0.026     1.105
  I              86          193         437     0.042    0.036     1.152
  K             158          439         523     0.076    0.082     0.930
  L             149          308         684     0.072    0.058     1.250
  M              23           72         152     0.011    0.013     0.826
  N              94          313         407     0.045    0.058     0.776
  P             135          328         411     0.065    0.061     1.064
  Q              99          252         332     0.048    0.047     1.015
  R             106          314         394     0.051    0.058     0.873
  S             168          429         553     0.081    0.080     1.012
  T             141          401         522     0.068    0.075     0.909
  V             128          239         515     0.062    0.045     1.383
  W              19           55         103     0.009    0.010     0.893
  X             118          306         453     0.057    0.057     1.025
  Y              71          158         245     0.034    0.029     1.161
  Z             119          342         433     0.058    0.064     0.916
Total          2066         5340        7944

Notes

Application of this method to a large number of proteins has shown that their method can predict antigenic determinants with about 75% accuracy which is better than most of the known methods.

References

  1. Kolaskar,AS and Tongaonkar,PC (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters 276: 172-174.
  2. Parker,JMR, Guo,D and Hodges,RS (1986). Biochemistry 25: 5425-5432.

Warnings

The program will warn you if the sequence is not a protein or has ambiguity codes.

Diagnostic Error Messages

Exit status

It exits with status 0.

Known bugs

None.

Author(s)

Original program "ANTIGENIC" by Peter Rice (EGCG 1991)

History

Target users

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