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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 2005 Nucleic Acids Research relative solvent accessibility Physical
DiscoTope 1.0 Web system
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 2008 Bioinformatics DiscoTope features and side chain direction RSA and HSE Physical
ElliPro Web system 2008 BMC Bioinformatics Protrusion index (Elliptical surface) Physical
PEPOP 2008 BMC Bioinformatics ASA and epitope sequence Physical
SEPPA Web system 2009 Nucleic Acids Research Amino acid propensity, clustering coefficient, ASA Physical +Chemical +Triangulation
Epitopia Web system 2009 BMC Bioinformatics 44 structure features and 41sequence feature with Naïve Bayes classifier Physical +Chemical + machine learning
EPCES Web system 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
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 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 2011 Computational Biology Bioinformatics Amino Acid pair and contact residue pairs with HMM Physical + Antibody info. + machine learning
DiscoTope 2.0 Web system 2012 PLOS ONE Amino Acid pair and RSA Physical + different host
Wen Zhang’s 2012 PLOS ONE Combine 6 CE systems and 4 LE systems Multiple system
PatchTope 2012 American Journal of Bioinformatics Research Surface patch for RSA and b factor with SVM Physical +Chemical + machine learning
CE-KEG Web system 2013 BMC Bioinformatics Energy and amino acid pair Physical +Chemical
SEPPA2.0 Web system 2014 Nucleic Acids Research RSA, clustering coefficient, ASA, AAindex for ANN with logistic regression Physical +Chemical
EpiPred Web system
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 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 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