CEP: a conformational epitope prediction server

By U. Kulkarni-Kale, S. Bhosle, A. Kolaskar. Nucleic Acids Res., 2005

314 citations recorded by the source corpus.

CEP server () provides a web interface to the conformational epitope prediction algorithm developed in-house. The algorithm, apart from predicting conformational epitopes, also predicts antigenic determinants and sequential epitopes. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. The algorithm employs structure-based Bioinformatics approach and solvent accessibility of amino acids in an explicit manner. Accuracy of the algorithm was found to be 75% when evaluated using X-ray crystal structures of Ag–Ab complexes available in the PDB. This is the first and the only method available for the prediction of conformational epitopes, which is an attempt to map probable antibody-binding sites of protein antigens.

Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/e0f38179ff3063055eee87ceca065bf02728271f

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Citations in the corpus

Fundamentals and Methods for T- and B-Cell Epitope Prediction (2017, background): “The first to be introduced was CEP [118], which relied almost entirely on predicting patches of solvent-exposed residues.”
Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network (2006, methodology): “12 Prediction of immunogenic epitopes remains vital and challenging task using bioinformatic tools.”
ElliPro: a new structure-based tool for the prediction of antibody epitopes (2008, methodology): “ElliPro has been tested on a benchmark dataset of epitopes inferred from 3D structures of antibody-protein complexes [11] and compared with six structure-based methods, including the only two existing methods developed specifically for epitope prediction, CEP [12] and DiscoTope [13]; two protein-pro”
Prediction of residues in discontinuous B‐cell epitopes using protein 3D structures (2006, methodology): “Recently, two new methods using protein structure and surface exposure for prediction of B-cell epitopes have been published ( Kulkarni-Kale et al. 2005; Batori et al. 2006).”
Template-based protein structure modeling using the RaptorX web server (2012, methodology): “For example, the predicted 3D models can be used for binding site 34 and epitope prediction 35 .”