Improved method for predicting linear B-cell epitopes.

Immunome Research
Jens Erik Pontoppidan LarsenMorten Nielsen

Abstract

B-cell epitopes are the sites of molecules that are recognized by antibodies of the immune system. Knowledge of B-cell epitopes may be used in the design of vaccines and diagnostics tests. It is therefore of interest to develop improved methods for predicting B-cell epitopes. In this paper, we describe an improved method for predicting linear B-cell epitopes. In order to do this, three data sets of linear B-cell epitope annotated proteins were constructed. A data set was collected from the literature, another data set was extracted from the AntiJen database and a data sets of epitopes in the proteins of HIV was collected from the Los Alamos HIV database. An unbiased validation of the methods was made by testing on data sets on which they were neither trained nor optimized on. We have measured the performance in a non-parametric way by constructing ROC-curves. The best single method for predicting linear B-cell epitopes is the hidden Markov model. Combining the hidden Markov model with one of the best propensity scale methods, we obtained the BepiPred method. When tested on the validation data set this method performs significantly better than any of the other methods tested. The server and data sets are publicly available at ht...Continue Reading

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Sep 2, 1985·FEBS Letters·G W WellingS Welling-Wester
Apr 8, 1985·Journal of Immunological Methods·J P BriandM H Van Regenmortel
Jun 3, 1988·Science·J A Swets
Jun 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·T P Hopp, K R Woods
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Apr 1, 1993·Immunology Letters·J L PellequerM H Van Regenmortel
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 11, 1999·Nucleic Acids Research·A Bairoch, R Apweiler
Jan 22, 2000·Arthritis and Rheumatism·G A SchellekensW J van Venrooij
Jan 31, 2003·Journal of Molecular Recognition : JMR·Michael Odorico, Jean-Luc Pellequer
Jul 23, 2003·Journal of Chemical Information and Computer Sciences·Helen McSparronDarren R Flower
Dec 4, 2004·Protein Science : a Publication of the Protein Society·Martin J Blythe, Darren R Flower
Mar 12, 2005·PLoS Biology·Bjoern PetersAlessandro Sette
Nov 30, 2007·Bioinformatics·Claus LundegaardMorten Nielsen

❮ Previous
Next ❯

Citations

Aug 30, 2012·Archivum Immunologiae Et Therapiae Experimentalis·Swaminathan SethuJean Sathish
Sep 19, 2012·Cancer Immunology, Immunotherapy : CII·Pornpimol CharoentongZlatko Trajanoski
Aug 29, 2012·Parasitology Research·Myoung-Ro LeeWon-Ja Lee
Feb 19, 2011·Virologica Sinica·Ping ChenKang-Hong Hu
Mar 29, 2013·Nature Reviews. Drug Discovery·Jean G SathishB Kevin Park
Sep 13, 2012·Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment·T CucuB Devreese
Nov 30, 2007·Bioinformatics·Claus LundegaardMorten Nielsen
Nov 29, 2011·Bioinformatics·David R RileyHervé Tettelin
Jun 3, 2008·Nucleic Acids Research·Qing ZhangBjoern Peters
Dec 17, 2008·Protein Engineering, Design & Selection : PEDS·Michael J Sweredoski, Pierre Baldi
Mar 23, 2010·Protein Engineering, Design & Selection : PEDS·Shinji SogaNoriaki Hirayama
Sep 5, 2009·International Journal of Plant Genomics·Géraldine MitouDevrim Gozuacik
Jun 23, 2011·BMC Bioinformatics·Yulong WangParantu K Shah
Mar 14, 2013·BMC Bioinformatics·Scott Yi-Heng LinEmily Chia-Yu Su
Mar 16, 2011·Malaria Journal·Gabriela Arévalo-PinzónManuel A Patarroyo
Oct 8, 2013·Malaria Journal·Gabriela Arévalo-PinzónManuel A Patarroyo
Jan 9, 2008·Immunome Research·Johannes SollnerBernd Mayer
Feb 25, 2011·Bioinformation·Debmalya BarhAzevedo Vasco
Sep 23, 2009·Reproduction : the Official Journal of the Society for the Study of Fertility·P M LokmanS Adachi
Dec 7, 2011·Reproduction : the Official Journal of the Society for the Study of Fertility·Purvi V MandeVrinda V Khole
Aug 24, 2013·Computational and Mathematical Methods in Medicine·Pingping SunYuxin Li
Apr 7, 2010·Journal of Biomedicine & Biotechnology·Salvador Eugenio C Caoili
Dec 12, 2013·Parasite : Journal De La Société Française De Parasitologie·Deying YangGuangyou Yang
Jun 21, 2014·International Journal of Molecular Sciences·Bee Yin KhorYee Siew Choong
Jan 1, 2007·Expert Opinion on Drug Discovery·Matthew N DaviesDarren R Flower
Mar 1, 2016·Frontiers in Microbiology·Patrycja A KobiereckaAgnieszka K Wyszyńska

❮ Previous
Next ❯

Software Mentioned

JenPep
BEPITOPE
AntiJen
PEOPLE
BepiPred
Alix

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Protein Science : a Publication of the Protein Society
Pernille Haste AndersenOle Lund
Journal of Molecular Recognition : JMR
Johannes Söllner, Bernd Mayer
Journal of Molecular Recognition : JMR
Michael Odorico, Jean-Luc Pellequer
Nucleic Acids Research
Avner SchlessingerBurkhard Rost
© 2022 Meta ULC. All rights reserved