ArticleBMC bioinformatics2011
MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Computational Methods in Immunoinformatics: Epitope Discovery and Diagnostic Applications.ACS omega · 2025Review
- Computational identification of antibody-binding epitopes from mimotope datasets.Frontiers in bioinformatics · 2024Article
- Statistical Analysis and Tokenization of Epitopes to Construct Artificial Neoepitope Libraries.ACS synthetic biology · 2023Article
- Review
- A Promising Tool in Serological Diagnosis: Current Research Progress of Antigenic Epitopes in Infectious Diseases.Pathogens (Basel, Switzerland) · 2022Review
- Understanding and Modulating Antibody Fine Specificity: Lessons from Combinatorial Biology.Antibodies (Basel, Switzerland) · 2022Review
- Current and prospective computational approaches and challenges for developing COVID-19 vaccines.Advanced drug delivery reviews · 2021Review
- Deimmunization of protein therapeutics - Recent advances in experimental and computational epitope prediction and deletion.Computational and structural biotechnology journal · 2021Review
- Phage display peptide libraries: deviations from randomness and correctives.Nucleic acids research · 2018Article
- Fundamentals and Methods for T- and B-Cell Epitope Prediction.Journal of immunology research · 2017Review
- The Relationship between B-cell Epitope and Mimotope Sequences.Protein and peptide letters · 2016Article
- Identification of a novel linear epitope on the NS1 protein of avian influenza virus.BMC microbiology · 2015Article
- Conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis.BioMed research international · 2015Article
- Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method.BMC bioinformatics · 2014Article
- Mimotope vaccination for epitope-specific induction of anti-VEGF antibodies.BMC biotechnology · 2013Article
- Peptide-based vaccinology: experimental and computational approaches to target hypervariable viruses through the fine characterization of protective epitopes recognized by monoclonal antibodies and the identification of T-cell-activating peptides.Clinical & developmental immunology · 2013Review
- Identification of cytotoxic T lymphocyte epitopes on swine viruses: multi-epitope design for universal T cell vaccine.PloS one · 2013Article
- Epitope mapping of metuximab on CD147 using phage display and molecular docking.Computational and mathematical methods in medicine · 2013Article
- Bioinformatics resources and tools for conformational B-cell epitope prediction.Computational and mathematical methods in medicine · 2013Review
- Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures.Biochimica et biophysica acta · 2012Article
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6 authors.
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Abstract
backgroundA B-cell epitope is a group of residues on the surface of an antigen which stimulates humoral responses. Locating these epitopes on antigens is important for the purpose of effective vaccine design. In recent years, mapping affinity-selected peptides screened from a random phage display library to the native epitope has become popular in epitope prediction. These peptides, also known as mimotopes, share the similar structure and function with the corresponding native epitopes. Great effort has been made in using this similarity between such mimotopes and native epitopes in prediction, which has resulted in better outcomes than statistics-based methods can. However, it cannot maintain a high degree of satisfaction in various circumstances.
resultsIn this study, we propose a new method that maps a group of mimotopes back to a source antigen so as to locate the interacting epitope on the antigen. The core of this method is a searching algorithm that is incorporated with both dynamic programming (DP) and branch and bound (BB) optimization and operated on a series of overlapping patches on the surface of a protein. These patches are then transformed to a number of graphs using an adaptable distance threshold (ADT) regulated by an appropriate compactness factor (CF), a novel parameter proposed in this study. Compared with both Pep-3D-Search and PepSurf, two leading graph-based search tools, on average from the results of 18 test cases, MimoPro, the Web-based implementation of our proposed method, performed better in sensitivity, precision, and Matthews correlation coefficient (MCC) than both did in epitope prediction. In addition, MimoPro is significantly faster than both Pep-3D-Search and PepSurf in processing.
conclusionsOur search algorithm designed for processing well constructed graphs using an ADT regulated by CF is more sensitive and significantly faster than other graph-based approaches in epitope prediction. MimoPro is a viable alternative to both PepSurf and Pep-3D-Search for epitope prediction in the same kind, and freely accessible through the MimoPro server located at http://informatics.nenu.edu.cn/MimoPro.
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