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Table 1 Conformational epitope prediction system or algorithm analysis

From: Conformational epitope matching and prediction based on protein surface spiral features

System name Instructions year published Features and method Feature classify
CEP Web system http://196.1.114.49/cgi-bin/cep.pl 2005 Nucleic Acids Research relative solvent accessibility Physical
DiscoTope 1.0 Web system
http://tools.iedb.org/stools/discotope/discotope.do
2006 Protein Science Amino acid log-odds and contact numbers Physical
Rapberger’s Algorithm 2007 Journal of Molecular Recognition solvent accessibility, shape complementarity and binding energies Physical +Chemical
BEpro (PEPITO) Web system http://pepito.proteomics.ics.uci.edu 2008 Bioinformatics DiscoTope features and side chain direction RSA and HSE Physical
ElliPro Web system http://tools.immuneepitope.org/ellipro 2008 BMC Bioinformatics Protrusion index (Elliptical surface) Physical
PEPOP http://diagtools.sysdiag.cnrs.fr/PEPOP/ 2008 BMC Bioinformatics ASA and epitope sequence Physical
SEPPA Web system http://lifecenter.sgst.cn/seppa/ 2009 Nucleic Acids Research Amino acid propensity, clustering coefficient, ASA Physical +Chemical +Triangulation
Epitopia Web system http://epitopia.tau.ac.il 2009 BMC Bioinformatics 44 structure features and 41sequence feature with Naïve Bayes classifier Physical +Chemical + machine learning
EPCES Web system http://sysbio.unl.edu/EPCES/ 2009 BMC Bioinformatics residue epitope propensity, conservation score, sidechain energy score, contact number, surface planarity score, and secondary structure composition. Physical +Chemical
Soga’s Algorithm 2010 Protein Engineering Amino acid propensity, ASEP Physical
Bepar Algorithm 2010 BMC Structural Biology paratope-epitope interacting biclique and cooccurrent pattern of interacting residue pairs Physical +Antibody info.
CBTOPE Web system
http://osddlinux.osdd.net/raghava/cbtope/submit.php
2010 Immunome Research Binary profile of patterns (BPP) + Physico-chemical profile of patterns (PPP) + Composition profile of patterns (CPP) with SVM Physical +Chemical
EPSVR Web system http://sysbio.unl.edu/services/ 2010 BMC Bioinformatics EPCES feature with SVR Physical +Chemical + machine learning
EPMeta Software 2010 BMC Bioinformatics Combine EPSVR and others 5 system Multiple system
Bpredictor Software 2011 BMC Bioinformatics thick surface patch and amino acid frequency with random forest (RF) algorithm Physical + machine learning
Liu’s Algorithm 2011 Journal of Proteomics & Bioinformatics relative solvent accessibility and b factor with logistic regression Physical
ABepar http://155.69.2.25/~s080011/index.html 2011 Computational Biology Bioinformatics Amino Acid pair and contact residue pairs with HMM Physical + Antibody info. + machine learning
DiscoTope 2.0 Web system www.cbs.dtu.dk/services/DiscoTope/ 2012 PLOS ONE Amino Acid pair and RSA Physical + different host
Wen Zhang’s http://bcell.whu.edu.cn 2012 PLOS ONE Combine 6 CE systems and 4 LE systems Multiple system
PatchTope http://www.fci.cu.edu.eg:8080/PatchTope/ 2012 American Journal of Bioinformatics Research Surface patch for RSA and b factor with SVM Physical +Chemical + machine learning
CE-KEG Web system http://cekeg.cs.ntou.edu.tw 2013 BMC Bioinformatics Energy and amino acid pair Physical +Chemical
SEPPA2.0 Web system http://lifecenter.sgst.cn/seppa2/ 2014 Nucleic Acids Research RSA, clustering coefficient, ASA, AAindex for ANN with logistic regression Physical +Chemical
EpiPred Web system
http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/EpiPred.php
2014 Structure Bioinformatics geometric fitting and knowledge-based asymmetric antibody-antigen scoring,then using docking program to enhance prediction ability Physical +Chemical +docking program
Hu’s Algorithm 2014 BMC Bioinformatics Combine 4 CE systems and 4 LE systems Multiple system
CBEP http://59.73.198.144:8088/CBEP/ 2014 BioMed Research International evolutionary profile, secondary structure, disorder zone, dipeptide composition and physicochemical properties with multiple ML Multiple system + multiple machine learning
CeePre Algorithm 2014 BMC Bioinformatics B factor, Evolutionary, Amino acid log-odds with random forest Physical +Chemical +machine learning
PEASE Web system http://www.ofranlab.org/PEASE 2015 Structural bioinformatics surface accessibility, secondary structure, predicted disorder, predicted interaction hotspots, the amino acid considered, and amino acids neighboring in sequence with Random Forest Physical + machine learning + Antibody info.
Sun’s Algorithm 2015 Bio Research International EPCES features and mimotope knowledge to enhance prediction ability Physical +chemical + mimotope
PUPre Algorithm 2015 BMC Bioinformatics 209 features +PU learning Physical +Chemical + machine learning
SePre Algorithm 2017 BMC Genomics 239 features + two staged heterogenous learning method Physical +Chemical + multiple machine learning
SEPIa Algorithm 2017 BMC Bioinformatics 13 sequence-based features with naïve Bayesian and random forest classifier Physical +Chemical + multiple machine learning