MIMOX: A web tool for phage display based epitope mapping

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
BMC Bioinformatics (Impact Factor: 2.58). 02/2006; 7(1):451. DOI: 10.1186/1471-2105-7-451
Source: PubMed


Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them.
We present MIMOX, a free web tool that helps to map the native epitope of an antibody based on one or more user supplied mimotopes and the antigen structure. MIMOX was coded in Perl using modules from the Bioperl project. It has two sections. In the first section, MIMOX provides a simple interface for ClustalW to align a set of mimotopes. It also provides a simple statistical method to derive the consensus sequence and embeds JalView as a Java applet to view and manage the alignment. In the second section, MIMOX can map a single mimotope or a consensus sequence of a set of mimotopes, on to the corresponding antigen structure and search for all of the clusters of residues that could represent the native epitope. NACCESS is used to evaluate the surface accessibility of the candidate clusters; and Jmol is embedded to view them interactively in their 3D context. Initial case studies show that MIMOX can reproduce mappings from existing tools such as FINDMAP and 3DEX, as well as providing novel, rational results.
A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at

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Available from: Jian Huang, Sep 03, 2015
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    • "Method Online service (program) Brief notes FINDMAP [64] Not available Map motif to antigen sequence EPIMAP [65] Not available Improved version of FINDMAP MIMOP/MimAlign [66] Available upon request Based on four multiple sequence alignments MEPS [67] Surface mimicking peptides 3DEX [68] Not available Physicochemical neighborhood MIMOX [88] The first free web tool MIMOP/MimCons [66] Available upon request Clustering the mimotope sequences Mapitope [69] [70] "
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    ABSTRACT: Identification of epitopes which invoke strong humoral responses is an essential issue in the field of immunology. Localizing epitopes by experimental methods is expensive in terms of time, cost, and effort; therefore, computational methods feature for its low cost and high speed was employed to predict B-cell epitopes. In this paper, we review the recent advance of bioinformatics resources and tools in conformational B-cell epitope prediction, including databases, algorithms, web servers, and their applications in solving problems in related areas. To stimulate the development of better tools, some promising directions are also extensively discussed.
    Computational and Mathematical Methods in Medicine 07/2013; 2013(1217):943636. DOI:10.1155/2013/943636 · 0.77 Impact Factor
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    • "The MIMOX algorithm was used to search for similarities between the phage-displayed consensus motifs and accessible amino acids on the three-dimensional structure of the EGFR surface [31]. The algorithm is freely available as a web-based tool ( "
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    ABSTRACT: Cetuximab and panitumumab, two antibodies targeting the extracellular domain of the epidermal growth factor receptor (EGFR), are of major clinical importance particularly in the treatment of metastatic colorectal cancer. As patients may acquire resistance-mediating mutations within the extracellular EGFR domain, functional dissection of the exact binding sites of EGFR targeting antibodies may help predict treatment responses. We therefore assessed the epitope recognition of panitumumab by screening phage-displayed random cyclic 7mer and linear 12mer peptide libraries on this antibody. Phage screenings revealed two strong, potentially epitope-mimicking consensus motifs targeted by panitumumab. A computational approach was used to map the sequences back to the potential epitope region on domain III of EGFR. The presumed epitope regions (386)WPEXRT(391) and a biochemically similar though discontinuous region P349-F352-D355 on a neighboring loop of domain III could be confirmed as part of the functionally relevant binding site of panitumumab by site-directed mutational analysis. To more accurately differentiate the panitumumab epitope from the previously characterized cetuximab epitope, binding studies were performed on a broad range of additional mutants. Taken together, this analysis revealed two large, partially overlapping functional epitopes consisting of 17 critical amino acid positions. Four of these positions were selectively targeted by cetuximab (I467, S468, Q408, and H409), whereas another four were selectively recognized by panitumumab (W386, E388, R390, and T391). In view of the clinical significance of extracellular domain mutations, our data may help guide treatment decisions in selected patients receiving EGFR-targeted therapies.
    Neoplasia (New York, N.Y.) 11/2012; 14(11):1023-31. DOI:10.1593/neo.121242 · 4.25 Impact Factor
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    • "The first one is the motif-based group, which align a motif or consensus sequence to template structure. This group includes 3DEX (Schreiber, et al., 2005), MIMOX (Huang, et al., 2006) and the MimCons section of MIMOP program (Moreau, et al., 2006). The second group includes Mapitope (Bublil, et al., 2006; Bublil, et al., 2007; Enshell-Seijffers, et al., 2003; Tarnovitski, et al., 2006) and its derivatives (Denisov, et al., 2009; Denisova, et al., 2008; Denisova, et al., 2009; Denisova, et al., 2010). "
    Protein-Protein Interactions - Computational and Experimental Tools, 03/2012; , ISBN: 978-953-51-0397-4
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