Predictive estimation of protein linear epitopes by using the program PEOPLE

A single small segment (sequence recognition) or domain (conformation recog nition) of a protein could act as an antigen (antigenic determinant) vs an antibody. Epitopes of the first kind being a continuous segment along the s equence (linear), generally bent with a typical non-ordered structure (turn s and/or loops), can be predicted from the only knowledge of the primary st ructure. After reviewing the different algorithms, we present PEOPLE (Predi ctive Estimation Of Protein Linear Epitopes) which uses combined prediction methods, taking into account the basic fundamental properties correspondin g to what should be an ideal epitope: bent (secondary structure mainly beta -turns), surface accessible, hydrophilic and mobile and/or flexible. Four c lasses of basic biophysical parameters are considered for the determination of an antigenic index AG - secondary structure; hydrophilicity; surface ac cessibility; flexibility. The AG index is finally defined as a linear combi nation of the four class profiles. Typical applications are presented. (C) 1999 Elsevier Science Ltd. All rights reserved.