Prediction of B cell epitopes in proteins using a novel sequence similarity-based method

Machine learning models and over-fitting considerations

(2022) Paris Charilaou et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface

(2021) Kosmas A. Galanis et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Prediction of unconventional protein secretion by exosomes

(2021) Alvaro Ras-Carmona et al.   BMC BIOINFORMATICS

BCEPS: A Web Server to Predict Linear B Cell Epitopes with Enhanced Immunogenicity and Cross-Reactivity

(2021) Alvaro Ras-Carmona et al.   Cells

Deep learning methods improve linear B-cell epitope prediction

(2020) Tao Liu et al.   BioData Mining

Potential Cross-Reactive Immunity to SARS-CoV-2 From Common Human Pathogens and Vaccines

(2020) Pedro A. Reche   Frontiers in Immunology

iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features

(2020) Md. Mehedi Hasan et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

(2019) Michael Schantz Klausen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Exploring the limitations of biophysical propensity scales coupled with machine learning for protein sequence analysis

(2019) Daniele Raimondi et al.   Scientific Reports

Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy

(2019) Monica J. Quinzo et al.   BMC BIOINFORMATICS

CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens

(2018) Tianyi Qiu et al.   Nature Communications

iBCE-EL: A New Ensemble Learning Framework for Improved Linear B-Cell Epitope Prediction

(2018) Balachandran Manavalan et al.   Frontiers in Immunology

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

PTML Model for Proteome Mining of B-Cell Epitopes and Theoretical–Experimental Study of Bm86 Protein Sequences from Colima, Mexico

(2017) Saúl G. Martínez-Arzate et al.   JOURNAL OF PROTEOME RESEARCH

A study of the Immune Epitope Database for some fungi species using network topological indices

(2017) Severo Vázquez-Prieto et al.   MOLECULAR DIVERSITY

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

(2017) Martin Closter Jespersen et al.   NUCLEIC ACIDS RESEARCH

Computer-Aided Design of an Epitope-Based Vaccine against Epstein-Barr Virus

(2017) Julio Alonso-Padilla et al.   Journal of Immunology Research

Fundamentals and Methods for T- and B-Cell Epitope Prediction

(2017) Jose L. Sanchez-Trincado et al.   Journal of Immunology Research

Immunoinformatics and epitope prediction in the age of genomic medicine

(2015) Linus Backert et al.   Genome Medicine

EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression

(2014) Yao Lian et al.   BMC BIOINFORMATICS

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Model for Vaccine Design by Prediction of B-Epitopes of IEDB Given Perturbations in Peptide Sequence, In Vivo Process, Experimental Techniques, and Source or Host Organisms

(2014) Humberto González-Díaz et al.   Journal of Immunology Research

Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence

(2013) Harinder Singh et al.   PLoS One

SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity

(2012) Bo Yao et al.   PLoS One

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Predicting linear B‐cell epitopes using string kernels

(2008) Yasser EL‐Manzalawy et al.   JOURNAL OF MOLECULAR RECOGNITION

COBEpro: a novel system for predicting continuous B-cell epitopes

(2008) Michael J. Sweredoski et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Benchmarking B cell epitope prediction: Underperformance of existing methods

(2004) Martin J. Blythe et al.   PROTEIN SCIENCE