CLC Main Workbench can help to identify antigenic regions in protein sequences in different ways, using different algorithms. The algorithms provided in the Workbench, merely plot an index of antigenicity over the sequence.
Two different methods are available.
[Welling et al., 1985] Welling et al. used information on the relative occurrence of amino acids in antigenic regions to make a scale which is useful for prediction of antigenic regions. This method is better than the Hopp-Woods scale of hydrophobicity which is also used to identify antigenic regions.
A semi-empirical method for prediction of antigenic regions has been developed [Kolaskar and Tongaonkar, 1990]. This method also includes information of surface accessibility and flexibility and at the time of publication the method was able to predict antigenic determinants with an accuracy of 75%.
Note! Similar results from the two method can not always be expected as the two methods are based on different training sets.