Pepitope: Epitope Mapping from Affinity-selected Peptides

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2007 Nov 6

PMID 17977889

Citations 54

Authors

Itay Mayrose

Osnat Penn

Elana Erez

Nimrod D Rubinstein

Tomer Shlomi

Natalia Tarnovitski Freund

Erez M Bublil

Eytan Ruppin

Roded Sharan

Jonathan M Gershoni

Eric Martz

Tal Pupko

Affiliations

Soon will be listed here.

Abstract

Unlabelled: Identifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure.

Availability: http://pepitope.tau.ac.il/

Citing Articles

Advances of computational methods enhance the development of multi-epitope vaccines.

Wei Y, Qiu T, Ai Y, Zhang Y, Xie J, Zhang D Brief Bioinform. 2025; 26(1).

PMID: 39951549 PMC: 11827616. DOI: 10.1093/bib/bbaf055.

Computational epitope-based vaccine design with bioinformatics approach; a review.

Basmenj E, Pajhouh S, Ebrahimi Fallah A, Naijian R, Rahimi E, Atighy H Heliyon. 2025; 11(1):e41714.

PMID: 39866399 PMC: 11761309. DOI: 10.1016/j.heliyon.2025.e41714.

A Novel Serum-Based Diagnosis of Alzheimer's Disease Using an Advanced Phage-Based Biochip.

Rizzo M, De Plano L, Palermo N, Franco D, Nicolo M, Sciuto E Adv Sci (Weinh). 2023; 10(21):e2301650.

PMID: 37150869 PMC: 10375152. DOI: 10.1002/advs.202301650.

Combination of Experimental and Bioinformatic Approaches for Identification of Immunologically Relevant Protein-Peptide Interactions.

Debeljak J, Korosec P, Selb J, Rijavec M, Kosnik M, Lunder M Biomolecules. 2023; 13(2).

PMID: 36830679 PMC: 9953301. DOI: 10.3390/biom13020310.

Current Update on Rotavirus in-Silico Multiepitope Vaccine Design.

Kuri P, Goswami P ACS Omega. 2023; 8(1):190-207.

PMID: 36643547 PMC: 9835168. DOI: 10.1021/acsomega.2c07213.

References

Enshell-Seijffers D, Denisov D, Groisman B, Smelyanski L, Meyuhas R, Gross G . The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1. J Mol Biol. 2003; 334(1):87-101. DOI: 10.1016/j.jmb.2003.09.002. View

Tarnovitski N, Matthews L, Sui J, Gershoni J, Marasco W . Mapping a neutralizing epitope on the SARS coronavirus spike protein: computational prediction based on affinity-selected peptides. J Mol Biol. 2006; 359(1):190-201. PMC: 7094247. DOI: 10.1016/j.jmb.2006.03.008. View

Halperin I, Wolfson H, Nussinov R . SiteLight: binding-site prediction using phage display libraries. Protein Sci. 2003; 12(7):1344-59. PMC: 2323941. DOI: 10.1110/ps.0237103. View

Sayle R . RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995; 20(9):374. DOI: 10.1016/s0968-0004(00)89080-5. View

Moreau V, Granier C, Villard S, Laune D, Molina F . Discontinuous epitope prediction based on mimotope analysis. Bioinformatics. 2006; 22(9):1088-95. DOI: 10.1093/bioinformatics/btl012. View

Villard S, Lacroix-Desmazes S, Kieber-Emmons T, Piquer D, Grailly S, Benhida A . Peptide decoys selected by phage display block in vitro and in vivo activity of a human anti-FVIII inhibitor. Blood. 2003; 102(3):949-52. DOI: 10.1182/blood-2002-06-1886. View

Schreiber A, Humbert M, Benz A, Dietrich U . 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J Comput Chem. 2005; 26(9):879-87. DOI: 10.1002/jcc.20229. View

Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J . SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Res. 2005; 33(Web Server issue):W39-43. PMC: 1160159. DOI: 10.1093/nar/gki398. View

Bublil E, Yeger-Azuz S, Gershoni J . Computational prediction of the cross-reactive neutralizing epitope corresponding to the [corrected] monclonal [corrected] antibody b12 specific for HIV-1 gp120. FASEB J. 2006; 20(11):1762-74. DOI: 10.1096/fj.05-5509rev. View

10.

Castrignano T, DOnorio De Meo P, Carrabino D, Orsini M, Floris M, Tramontano A . The MEPS server for identifying protein conformational epitopes. BMC Bioinformatics. 2007; 8 Suppl 1:S6. PMC: 1885858. DOI: 10.1186/1471-2105-8-S1-S6. View

11.

Irving M, Pan O, Scott J . Random-peptide libraries and antigen-fragment libraries for epitope mapping and the development of vaccines and diagnostics. Curr Opin Chem Biol. 2001; 5(3):314-24. PMC: 7129944. DOI: 10.1016/s1367-5931(00)00208-8. View

12.

Mayrose I, Shlomi T, Rubinstein N, Gershoni J, Ruppin E, Sharan R . Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res. 2006; 35(1):69-78. PMC: 1761437. DOI: 10.1093/nar/gkl975. View

13.

Tsodikov O, Record Jr M, Sergeev Y . Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem. 2002; 23(6):600-9. DOI: 10.1002/jcc.10061. View

14.

Bublil E, Freund N, Mayrose I, Penn O, Roitburd-Berman A, Rubinstein N . Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins. 2007; 68(1):294-304. DOI: 10.1002/prot.21387. View