Antibody Epitope Prediction Tutorial

I. Methods for predicting continuous antibody epitope from protein sequences

General basis: Parameters such as hydrophilicity, flexibility, accessibility, turns, exposed surface, polarity and antigenic propensity of polypeptides chains have been correlated with the location of continuous epitopes. This has led to a search for empirical rules that would allow the position of continuous epitopes to be predicted from certain features of the protein sequence. All prediction calculations are based on propensity scales for each of the 20 amino acids. Each scale consists of 20 values assigned to each of the amino acid residues on the basis of their relative propensity to possess the property described by the scale.

General method: When computing the score for a given residue i, the amino acids in an interval of the chosen length, centered around residue i, are considered. In other words, for a window size n, the i - (n-1)/2 neighboring residues on each side of residue i were used to compute the score for residue i. Unless specified, the score for residue i is the average of the scale values for these amino acids (see table 1 for specific method implementation details). In general, a window size of 5 to 7 is appropriate for finding regions that may potentially be antigenic.

Table 1. Implemented methods

Method

Chou and Fasman beta turn prediction

Emini surface accessibility scale
Karplus and Schulz flexibility scale
  • Reference: Karplus PA, Schulz GE. Prediction of Chain Flexibility in Proteins - A tool for the Selection of Peptide Antigens. Naturwissenschafren 1985; 72:212-3.
  • Description: In this method, flexibility scale based on mobility of protein segments on the basis of the known temperature B factors of the a-carbons of 31 proteins of known structure was constructed. The calculation based on a flexibility scale is similar to classical calculation, except that the center is the first amino acid of the six amino acids window length, and there are three scales for describing flexibility instead of a single one.
Kolaskar and Tongaonkar antigenicity scale
Parker Hydrophilicity Prediction
Bepipred Linear Epitope Prediction

II. Input

1. Enter a protein sequence in plain format

2. Select a prediction method

3. Click submit

Example Input

 

III. Output

Example Output
Example outpu t in table format