Abstract:
:A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This set of peptides is regarded as mimicking the genuine epitope of the antibody's interacting antigen and can be used to define it. Here we present PepSurf, an algorithm for mapping a set of affinity-selected peptides onto the solved structure of the antigen. The problem of epitope mapping is converted into the task of aligning a set of query peptides to a graph representing the surface of the antigen. The best match of each peptide is found by aligning it against virtually all possible paths in the graph. Following a clustering step, which combines the most significant matches, a predicted epitope is inferred. We show that PepSurf accurately predicts the epitope in four cases for which the epitope is known from a solved antibody-antigen co-crystal complex. We further examine the capabilities of PepSurf for predicting other types of protein-protein interfaces. The performance of PepSurf is compared to other available epitope mapping programs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Mayrose I,Shlomi T,Rubinstein ND,Gershoni JM,Ruppin E,Sharan R,Pupko Tdoi
10.1093/nar/gkl975subject
Has Abstractpub_date
2007-01-01 00:00:00pages
69-78issue
1eissn
0305-1048issn
1362-4962pii
gkl975journal_volume
35pub_type
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