About: Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
Creator	Braun, Werner
Source	Medline; PMC
abstract	BACKGROUND: Precise determination of conformational epitopes of neutralizing antibodies represents a key step in the rational design of novel vaccines. A powerful experimental method to gain insights on the physical chemical nature of conformational epitopes is the selection of linear peptides that bind with high affinities to a monoclonal antibody of interest by phage display technology. However, the structural characterization of conformational epitopes from these mimotopes is not straightforward, and in the past the interpretation of peptide sequences from phage display experiments focused on linear sequence analysis to find a consensus sequence or common sequence motifs. RESULTS: We present a fully automated search method, EpiSearch that predicts the possible location of conformational epitopes on the surface of an antigen. The algorithm uses peptide sequences from phage display experiments as input, and ranks all surface exposed patches according to the frequency distribution of similar residues in the peptides and in the patch. We have tested the performance of the EpiSearch algorithm for six experimental data sets of phage display experiments, the human epidermal growth factor receptor-2 (HER-2/neu), the antibody mAb Bo2C11 targeting the C(2) domain of FVIII, antibodies mAb 17b and mAb b12 of the HIV envelope protein gp120, mAb 13b5 targeting HIV-1 capsid protein and 80R of the SARS coronavirus spike protein. In all these examples the conformational epitopes as determined by the X-ray crystal structures of the antibody-antigen complexes, were found within the highest scoring patches of EpiSearch, covering in most cases more than 50% residues of experimental observed conformational epitopes. Input options of the program include mapping of a single peptide or a set of peptides on the antigen structure, and the results of the calculation can be visualized on our interactive web server. AVAILABILITY: Users can access the EpiSearch from our web server http://curie.utmb.edu/episearch.html
has issue date	2009-07-01(xsd:dateTime)
bibo:pmid	20140073
has license	cc-by
sha1sum (hex)	31b6292728805572de28133c6eb02ed1d44ef211
resource representing a document's title	Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
has PubMed Central identifier	PMC2808184
has PubMed identifier	20140073
schema:publication	Bioinform Biol Insights
resource representing a document's body	covid:31b6292728805572de28133c6eb02ed1d44ef211#body_text
is schema:about of	named entity 'PEPTIDE' named entity 'sequences' named entity 'vaccines' named entity 'focused' named entity 'insights' named entity 'selection' named entity 'sequences' named entity 'R C' named entity 'NOVEL' named entity 'SEQUENCES' named entity 'SEQUENCE ANALYSIS' named entity 'GAIN' named entity 'BIND' named entity 'STRAIGHTFORWARD' named entity 'PEPTIDE' named entity 'COMMON' named entity 'STEP' named entity 'DETERMINATION' named entity 'HIGH' named entity 'VACCINES' named entity 'DESIGN' named entity 'SELECTION' named entity 'POWERFUL' named entity 'INTERPRETATION' named entity 'EXPERIMENTAL METHOD' named entity 'STRUCTURAL CHARACTERIZATION' named entity 'THESE' named entity 'DISPLAY TECHNOLOGY' named entity 'BIOLOGY' named entity 'INSIGHTS' named entity 'FOCUSED' named entity 'PRECISE' named entity 'AFFINITIES' named entity 'PHYSICAL' named entity 'INSIGHTS' named entity 'PEPTIDES' named entity 'USING' named entity 'N A' named entity 'BIOINFORMATICS' named entity 'SEQUENCES' named entity 'IN THE PAST' named entity 'BACKGROUND' named entity 'CHEMICAL' named entity 'MONOCLONAL ANTIBODY' named entity 'CONSENSUS SEQUENCE' named entity 'KEY' named entity 'EXPERIMENTS' named entity 'PHAGE DISPLAY' named entity 'EPITOPES' named entity 'EPITOPES' named entity 'NEUTRALIZING ANTIBODIES' named entity 'NATURE' named entity 'DETECTION' named entity 'AUTOMATED' named entity 'OF INTEREST' named entity 'MIMOTOPES' named entity 'SEQUENCE MOTIFS' named entity 'LINEAR' named entity 'PHAGE DISPLAY' covid:arg/31b6292728805572de28133c6eb02ed1d44ef211 named entity 'neutralizing antibodies' named entity 'structural' named entity 'phage display' named entity 'interpretation' named entity 'epitopes' named entity 'phage display' named entity 'gain' named entity 'rational design' named entity 'peptide sequences' named entity 'experimental method' named entity 'protein sequence' named entity 'Conformational epitopes' named entity 'crystal structure' named entity 'binding energies' named entity 'cofactor' named entity 'mAb' named entity 'protein' named entity 'binding site' named entity 'phage display' named entity 'sequence homology' named entity 'phage display' named entity 'peptide sequences' named entity 'binding site'

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