Linear B-cell epitope prediction: a performance review of currently available methods

No abstract is available for this paper.

• Publication year

  2019

• Venue

  bioRxiv

• Publication date

  2019-11-07

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1101/833418
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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

  2018cited by this paper
• In silico prediction of T- and B-cell epitopes in PmpD: First step towards to the design of a Chlamydia trachomatis vaccine

  2018cited by this paper
• T-Cell Epitope Prediction.

  2017cited by this paper
• Ten quick tips for machine learning in computational biology

  2017cited by this paper
• DRREP: deep ridge regressed epitope predictor

  2017cited by this paper
• Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

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

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

  2017cited by this paper
• Improved topology prediction using the terminal hydrophobic helices rule

  2016cited by this paper
• Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-Based Feature Descriptor

  2015influential reference
• Predicting linear B-cell epitopes using amino acid anchoring pair composition

  2015cited by this paper
• An Improved Method for Predicting Linear B-cell Epitope Using Deep Maxout Networks.

  2015cited by this paper
• Immunoinformatics: a brief review.

  2014cited by this paper
• Antibody informatics for drug discovery.

  2014cited by this paper
• The immune epitope database (IEDB) 3.0

  2014influential reference
• EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression

  2014cited by this paper
• Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence

  2013influential reference
• Prediction of B-cell epitopes using evolutionary information and propensity scales

  2013cited by this paper
• An optimized algorithm for detecting and annotating regional differential methylation

  2013cited by this paper
• Using random forest to classify linear B-cell epitopes based on amino acid properties and molecular features.

  2013cited by this paper
• A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins

  2013cited by this paper
• Structural analysis of B-cell epitopes in antibody:protein complexes.

  2013cited by this paper
• BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences

  2012cited by this paper
• SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity

  2012influential reference
• Prediction of B-cell Linear Epitopes with a Combination of Support Vector Machine Classification and Amino Acid Propensity Identification

  2011cited by this paper
• Determinants of antigenicity and specificity in immune response for protein sequences

  2011cited by this paper
• Recent advances in B-cell epitope prediction methods

  2010cited by this paper
• SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction

  2010cited by this paper
• The Immune Epitope Database 2.0

  2009influential reference
• Epitope Mapping Protocols

  2009cited by this paper
• An in silico study of the molecular basis of B-RAF activation and conformational stability

  2009cited by this paper
• Prediction of linear B-cell epitopes.

  2009influential reference
• COBEpro: a novel system for predicting continuous B-cell epitopes.

  2009influential reference
• Epitope mapping protocols. Preface.

  2009cited by this paper
• Epitopia: a web-server for predicting B-cell epitopes

  2009cited by this paper
• Predicting Flexible Length Linear B-cell Epitopes

  2008cited by this paper
• Predicting linear B‐cell epitopes using string kernels

  2008cited by this paper
• Immunoinformatics and the in silico prediction of immunogenicity. An introduction.

  2007cited by this paper
• Immunoinformatics

  2007cited by this paper
• Towards a consensus on datasets and evaluation metrics for developing B‐cell epitope prediction tools

  2007influential reference
• Prediction of linear B-cell epitopes using amino acid pair antigenicity scale

  2007influential reference
• Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network

  2006cited by this paper
• Machine learning approaches for prediction of linear B‐cell epitopes on proteins

  2006cited by this paper
• Improved method for predicting linear B-cell epitopes

  2006influential reference
• A consensus epitope prediction approach identifies the breadth of murine TCD8+-cell responses to vaccinia virus

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• Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines

  2006cited by this paper
• SCRATCH: a protein structure and structural feature prediction server

  2005cited by this paper
• Benchmarking B cell epitope prediction: Underperformance of existing methods

  2005cited by this paper
• Bcipep: A database of B-cell epitopes

  2005influential reference
• AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data

  2005cited by this paper
• Minimizing the immunogenicity of protein therapeutics.

  2004cited by this paper
• UniProt: the Universal Protein knowledgebase

  2004cited by this paper
• A combined transmembrane topology and signal peptide prediction method.

  2004cited by this paper
• BcePred: Prediction of Continuous B-Cell Epitopes in Antigenic Sequences Using Physico-chemical Properties

  2004cited by this paper
• BEPITOPE: predicting the location of continuous epitopes and patterns in proteins

  2003cited by this paper
• Prediction of coordination number and relative solvent accessibility in proteins

  2002cited by this paper
• A Totally Synthetic Polyoxime Malaria Vaccine Containing Plasmodium falciparum B Cell and Universal T Cell Epitopes Elicits Immune Responses in Volunteers of Diverse HLA Types1

  2001cited by this paper
• The diagnostic properties of rheumatoid arthritis antibodies recognizing a cyclic citrullinated peptide.

  2000cited by this paper
• Predictive estimation of protein linear epitopes by using the program PEOPLE.

  1999cited by this paper
• Combinations of Weak Classifiers

  1996cited by this paper
• Ability of synthetic peptides representing epitopes of outer membrane protein F of Pseudomonas aeruginosa to afford protection against P. aeruginosa infection in a murine acute pneumonia model.

  1995cited by this paper
• PREDITOP: a program for antigenicity prediction.

  1993cited by this paper
• Correlation between the location of antigenic sites and the prediction of turns in proteins.

  1993cited by this paper
• Predicting location of continuous epitopes in proteins from their primary structures.

  1991cited by this paper
• A semi‐empirical method for prediction of antigenic determinants on protein antigens

  1990cited by this paper
• Vaccine engineering: enhancement of immunogenicity of synthetic peptide vaccines related to hepatitis in chemically defined models consisting of T- and B-cell epitopes.

  1989cited by this paper
• New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites.

  1986cited by this paper
• Continuous and discontinuous protein antigenic determinants

  1986cited by this paper
• Prediction of chain flexibility in proteins

  1985cited by this paper
• Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide

  1985cited by this paper
• Prediction of protein antigenic determinants from amino acid sequences.

  1981cited by this paper
• A simplified representation of protein conformations for rapid simulation of protein folding.

  1976cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper
• Bioinformatics Applications Note Sequence Analysis Cd-hit Suite: a Web Server for Clustering and Comparing Biological Sequences

  year unknowncited by this paper

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