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

An in silico deep learning approach to multi-epitope vaccine design: a SARS-CoV-2 case study

(2021) Zikun Yang et al.   Scientific Reports

Design an Efficient Multi-Epitope Peptide Vaccine Candidate Against SARS-CoV-2: An in silico Analysis

(2020) Zahra Yazdani et al.   Infection and Drug Resistance

Designing B- and T-cell multi-epitope based subunit vaccine using immunoinformatics approach to control Zika virus infection

(2018) Rajan Kumar Pandey et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

In silico prediction of T- and B-cell epitopes in PmpD: First step towards to the design of a Chlamydia trachomatis vaccine

(2018) Romina Cecilia Russi et al.   Biomedical Journal

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

(2018) Balachandran Manavalan et al.   Frontiers in Immunology

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

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

Ten quick tips for machine learning in computational biology

(2017) Davide Chicco   BioData Mining

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

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

Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

(2017) Sabri Boughorbel et al.   PLoS One

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Improved topology prediction using the terminal hydrophobic helices rule

(2015) Christoph Peters et al.   BIOINFORMATICS

Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-Based Feature Descriptor

(2015) Vijayakumar Saravanan et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Predicting linear B-cell epitopes using amino acid anchoring pair composition

(2015) Weike Shen et al.   BioData Mining

Antibody informatics for drug discovery

(2014) Hiroki Shirai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Using random forest to classify linear B-cell epitopes based on amino acid properties and molecular features

(2014) Jian-Hua Huang et al.   BIOCHIMIE

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

Conformational B-Cell Epitopes Prediction from Sequences Using Cost-Sensitive Ensemble Classifiers and Spatial Clustering

(2014) Jian Zhang et al.   Biomed Research International

Prediction of B-cell epitopes using evolutionary information and propensity scales

(2013) Scott Lin et al.   BMC BIOINFORMATICS

A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins

(2013) Antonios C. Tsolis et al.   PLoS One

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

(2013) Harinder Singh et al.   PLoS One

Structural analysis of B-cell epitopes in antibody:protein complexes

(2012) Jens Vindahl Kringelum et al.   MOLECULAR IMMUNOLOGY

BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences

(2012) Jianzhao Gao 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

Determinants of antigenicity and specificity in immune response for protein sequences

(2011) Yulong Wang et al.   BMC BIOINFORMATICS

Prediction of B-cell Linear Epitopes with a Combination of Support Vector Machine Classification and Amino Acid Propensity Identification

(2011) Hsin-Wei Wang et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction

(2010) Lawrence JK Wee et al.   BMC GENOMICS

Epitope Discovery and Their Use in Peptide Based Vaccines

(2010) Nadine L. Dudek et al.   CURRENT PHARMACEUTICAL DESIGN

Identification of major antigenic peptide of filarial glutathione-S-transferase

(2010) Marshleen Yadav et al.   VACCINE

Epitopia: a web-server for predicting B-cell epitopes

(2009) Nimrod D Rubinstein et al.   BMC BIOINFORMATICS

Prediction of linear B-cell epitopes

(2009) Ya. I. Davydov et al.   MOLECULAR BIOLOGY

The Immune Epitope Database 2.0

(2009) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Amyloidogenic determinants are usually not buried

(2009) Kimon K Frousios et al.   BMC STRUCTURAL BIOLOGY

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