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Proceedings Paper

Computer-based optimization of high-throughput peptide screening
Author(s): Peter J. van der Veen; Lodewyk F. A. Wessels; Jerry W. Slootstra; Rob H. Meloen; Marcel J. T. Reinders; J. Hellendoorn
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Paper Abstract

Four different algorithms are presented which generate potentially well biding peptides against specific mono- clonal antibodies. The input data for these algorithms comes form random peptide array screening experiments, which results in a binding strength for a few thousand peptides against the antibody. The first algorithm identifies short motifs of amino acids which occur more frequently among the best binding peptides than among the worst binding ones. The second algorithm differs from this algorithm in the sense that it searches for amino acids in the best binding peptides, regardless of the order of these amino acids. The fourth algorithm replaces all amino acids by a hydrophilicity value and starts to search for clusters in the profiles of the best measured results. Results obtained from experimental data show that the algorithms are able to generate peptides which obtain a resemblance with the peptides which are known to bind reasonably well against these antibodies. The information gained from these algorithms is useful for the design of subsequent experiments aimed at further optimization of the best binding peptides found during the peptide screening experiment.

Paper Details

Date Published: 21 June 2002
PDF: 12 pages
Proc. SPIE 4626, Biomedical Nanotechnology Architectures and Applications, (21 June 2002); doi: 10.1117/12.472119
Show Author Affiliations
Peter J. van der Veen, Delft Univ. of Technology (Netherlands)
Lodewyk F. A. Wessels, Delft Univ. of Technology (Netherlands)
Jerry W. Slootstra, Pepscan Systems BV (Netherlands)
Rob H. Meloen, Pepscan Systems BV (Netherlands)
Marcel J. T. Reinders, Delft Univ. of Technology (Netherlands)
J. Hellendoorn, Delft University of Technology (Netherlands)


Published in SPIE Proceedings Vol. 4626:
Biomedical Nanotechnology Architectures and Applications
Raymond P. Mariella; Catherine J. Murphy; Michelle Palmer; David A. Dunn; Darryl J. Bornhop; David A. Dunn; Raymond P. Mariella; Catherine J. Murphy; Dan V. Nicolau; Shuming Nie; Michelle Palmer; Ramesh Raghavachari; Darryl J. Bornhop; Ramesh Raghavachari; Shuming Nie; Ramesh Raghavachari, Editor(s)

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