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On the Surface or Not?

Core antigen for Hepatitis B virus.

Multiple known epitopes, covering >50% of the molecule (130 aa from 183) are surface-exposed. The predictions of their surface exposure by 3 algorithms were compared.

NS1 of Degue Virus 2

Here the established epitopes include only 93 aa form 380 of the  total 380; whether any other sequences are exposed or not - unknown. Therefore, the ideal prediction program should identify as many as possible of aa from known epitopes, ans misidentify as hidden as few as possible. Clearly, EpiQuest-A perfoms much better. 

EpiQuest™-A

Especially when developing antibodies that can recognize the native protein, it is important to predict which domains of the molecule are accessible, and which are not.

 

All current surface exposure/accessibility prediction programs are based on either Emini or Janin algorithms. In our experience, they often miss (both algorithms) or wrongly identify the exposure of the peptides on the surface of the molecule. Therefore, we have developed EpiQuest A (for accessibility) to be used together with B-epitope prediction program EpiQuest-B.

 

As our primary aim is to predict epitope accessibility for an antibody, one way to evaluate the program is to take molecules with known immunodominant epitopes, recognized by antibodies reactive with the intact molecule, and to see, whether the sequence of the epitope will be included with a respective software into surface-exposed or into non-accessible (from the surface) domain.

 

We used Emin and Janin analysis as presented elsewhere, and analysed the correlation of the predicted accessibility to the experimentally obtained. Obviously, this can be done in accessible areas only; ideally, the program should identify as many proven accessible amino acids (sensitivity) while assigning accessibility to the minimal number of regions (specificity).

 

The provided data illustrate, that although the algorithm of Janin has high specificity, it is achieved by severe sacrifice of sensitivity. For widely used Emini algorithm, both parameters are clearly inferior comparing to EpiQuest-A.

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Bovine Casein

Only one area with exposed epitopes is established for Casein; it is only 32 aa form 251aa of the entire molecule. According to Janin algorithm this area is not exposed at all; according to Emini - over 2/3 of it is inaccessible at the sruface. Using these algorithms you would not expect an epitope in this area at all.

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