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Despite the high specificity between antigen and antibody binding, similar epitopes can be recognized or cross-neutralized by paratopes of antibody with different binding affinities. How to accurately characterize this slight variation which may or may not change the antigen-antibody binding affinity is a key issue in this area. In this report, by combining cylinder model with shell structure model, a new fingerprint was introduced to describe both the structural and physical-chemical features of the antigen and antibody protein. Furthermore, beside the description of individual protein, the specific epitope-paratope interaction fingerprint (EPIF) was developed to reflect the bond and the environment of the antigen-antibody interface. Finally, Proteochemometric Modeling of the antigen-antibody interaction was established and evaluated on 429 antigen-antibody complexes. By using only protein descriptors, our model achieved the best performance (R  2  =  0.91  ,   Q   t  e  s  t   2   =  0.68) among peers. Further, together with EPIF as a new cross-term, our model (R  2  =  0.92  ,   Q   t  e  s  t   2   =  0.74) can significantly outperform peers with multiplication of ligand and protein descriptors as a cross-term (R  2  ≤  0.81  ,   Q   t  e  s  t   2   ≤  0.44). Results illustrated that: 1) our newly designed protein fingerprints and EPIF can better describe the antigen-antibody interaction; 2) EPIF is a better and specific cross-term in Proteochemometric Modeling for antigen-antibody interaction. The fingerprints designed in this study will provide assistance to the description of antigen-antibody binding, and in future, it may be valuable help for the high-throughput antibody screening. The algorithm is freely available on request.

Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction