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      SAROTUP: Scanner and Reporter of Target-Unrelated Peptides

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          Abstract

          As epitope mimics, mimotopes have been widely utilized in the study of epitope prediction and the development of new diagnostics, therapeutics, and vaccines. Screening the random peptide libraries constructed with phage display or any other surface display technologies provides an efficient and convenient approach to acquire mimotopes. However, target-unrelated peptides creep into mimotopes from time to time through binding to contaminants or other components of the screening system. In this study, we present SAROTUP, a free web tool for scanning, reporting and excluding possible target-unrelated peptides from real mimotopes. Preliminary tests show that SAROTUP is efficient and capable of improving the accuracy of mimotope-based epitope mapping. It is also helpful for the development of mimotope-based diagnostics, therapeutics, and vaccines.

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          Most cited references36

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          Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface.

          G. Smith (1985)
          Foreign DNA fragments can be inserted into filamentous phage gene III to create a fusion protein with the foreign sequence in the middle. The fusion protein is incorporated into the virion, which retains infectivity and displays the foreign amino acids in immunologically accessible form. These "fusion phage" can be enriched more than 1000-fold over ordinary phage by affinity for antibody directed against the foreign sequence. Fusion phage may provide a simple way of cloning a gene when an antibody against the product of that gene is available.
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            PDBsum new things

            PDBsum (http://www.ebi.ac.uk/pdbsum) provides summary information about each experimentally determined structural model in the Protein Data Bank (PDB). Here we describe some of its most recent features, including figures from the structure's key reference, citation data, Pfam domain diagrams, topology diagrams and protein–protein interactions. Furthermore, it now accepts users’ own PDB format files and generates a private set of analyses for each uploaded structure.
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              A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.

              Peptide recognition modules mediate many protein-protein interactions critical for the assembly of macromolecular complexes. Complete genome sequences have revealed thousands of these domains, requiring improved methods for identifying their physiologically relevant binding partners. We have developed a strategy combining computational prediction of interactions from phage-display ligand consensus sequences with large-scale two-hybrid physical interaction tests. Application to yeast SH3 domains generated a phage-display network containing 394 interactions among 206 proteins and a two-hybrid network containing 233 interactions among 145 proteins. Graph theoretic analysis identified 59 highly likely interactions common to both networks. Las17 (Bee1), a member of the Wiskott-Aldrich Syndrome protein (WASP) family of actin-assembly proteins, showed multiple SH3 interactions, many of which were confirmed in vivo by coimmunoprecipitation.
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                Author and article information

                Journal
                J Biomed Biotechnol
                JBB
                Journal of Biomedicine and Biotechnology
                Hindawi Publishing Corporation
                1110-7243
                1110-7251
                2010
                21 March 2010
                : 2010
                Affiliations
                Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
                Author notes

                Academic Editor: Yongqun Oliver He

                Article
                10.1155/2010/101932
                2842971
                20339521
                9779cc21-1b66-4c3a-9b52-c133e9aae6c4
                Copyright © 2010 Jian Huang et al.

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Research Article

                Molecular medicine
                Molecular medicine

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