title: Selection of protein epitopes for antibody production.
abstract: Protein functional analysis in the post-genomic era is a huge task that has to be approached by different methods in parallel. The use of protein-specific antibodies in conjunction with tissue microarrays has proven to be one important technology. In this study, we present a strategy for the optimized design of protein subfragments for subsequent antibody production. The fragments are selected based on a principle of lowest sequence similarity to other human proteins, optimally to generate antibodies with high selectivity. Furthermore, the fragments should have properties optimized for efficient protein production in Escherichia coli. The strategy has been implemented in Bishop, which is a Java-based software enabling the high-throughput production of protein fragments. Bishop allows for the avoidance of certain restriction enzyme sites, transmembrane regions, and signal peptides. A Basic Local Alignment Search Tool (BLAST) scanning procedure permits the selection of fragments of a selected size with a minimal sequence similarity to other proteins. The software and the strategy were evaluated on a human test data set and verified to fulfill the requested criteria.
authors.affiliation: Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Mats
authors.initials: M
authors.lastname: Lindskog
authors.forename: Johan
authors.initials: J
authors.lastname: Rockberg
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlén
authors.forename: Fredrik
authors.initials: F
authors.lastname: Sterky
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000917:Antibody Formation; D001665:Binding Sites; D018604:Epitope Mapping / Q000379:methods*; D008969:Molecular Sequence Data; D011485:Protein Binding; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software