Epithelial Systems Biology Laboratory

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Integrated Antibody Design

Since the early 1990's, members of the Knepper Lab have been producing peptide-directed polyclonal antibodies to the major renal solute and water transporters expressed along the renal tubule for use in studies of renal physiology (4). The Knepper Laboratory has shared its antibodies with laboratories throughout the world. This experience led to a general protocol for the identification of optimal synthetic peptide sequences that are immunogenic, unique, and free of post-translational modifications that could alter the epitope in the target protein (4). Because this general protocol for antibody design required use of multiple computer programs, its application was awkward and slow. To remedy the situation, we built a data-consolidating program called NHLBI-AbDesigner that simultaneously displays all of the data required to choose an optimal synthetic peptide sequence for immunization (2, 3). Because of the usefulness of AbDesigner in our own projects, we made it available to the general public through a Java-based online application accessible at https://hpcwebapps.cit.nih.gov/AbDesigner/. AbDesigner is now widely used by many commercial entities as well as academic institutions. AbDesigner is an early example of application of the Big Data concept in which comprehensive data sets from numerous sources are consolidated to create a multi-source information tool. An updated version called AbDesigner3D has recently been introduced (1) to incorporate 3D structural data in the prediction of optimal target peptides for antibody production.

Knepper Laboratory antibodies can be obtained through this link.


  1. Saethang T, Hodge K, Kimkong I, Payne DM, Knepper MA, Pisitkun T. AbDesigner3D: a structure-guided tool for peptide-based antibody production. Bioinformatics. 2018; 34: 2158-2160. PMID: 29408997.

  2. Pisitkun T, Dummer P, Somparn P, Hirankarn N, Kopp JB, Knepper MA. Integrated design of antibodies for systems biology using AbDesigner. J Proteomics Bioinform. 2014; 7: 088-94. PMID: 25328345.

  3. Pisitkun T, Hoffert JD, Saeed F, Knepper MA. NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies. Am J Physiol Cell Physiol. 2012; 302: C154-64. PMID: 21956165.

  4. Knepper MA, Masilamani S. Targeted proteomics in the kidney using ensembles of antibodies. Physiol Scand. 2001; 173: 11-21. PMID: 11678722.