Table 1.
Linear B-cell epitope predictors in chronological order, alongside a short description of their methodology, their current status and their web page. After researching the relevant publications, we gathered up all the linear B-cell epitopes predictors we could find in this fairly complete, but not exhaustive catalogue. For every method we reference the source material to determine their methodology, which we have summed up for each predictor in a short description. For every predictor we also checked their availability status, as of writing this review, and categorized them regarding their general and current availability online as tools, as well as their obtainability as standalone software packages. We also provide the institution in which they were developed. In the last column, we provide the website links for each method, when available.
| Predictor | Description | Status | Institution | Link |
|---|---|---|---|---|
| Antigenic [24] | Physico-chemical propensity scales, occurrence of residues | Not currently available online | Department of Zoology, University of Poona, India | http://www.emboss.bioinformatics.nl/cgi-bin/emboss/antigenic |
| PEOPLE [29] | Physico-chemical propensity scales | Not available online | Laboratoire de Spectroscopies et Structures Biomoléculaire, Université de Reims Champagne Ardenne, France | - |
| BEPITOPE [30] | Physico-chemical propensity scales | Freely available online | Ιnstitute of environmental biology and biotechnology, CEA, France | http://bepitope.ibs.fr/ |
| BcePred [31] | Physico-chemical propensity scales | Freely available online and downloadable | Ιnstitute of Microbial Technology, Chandigarh, Ιndia | http://crdd.osdd.net/raghava/bcepred/index.html |
| BepiPred-1.0 [33] | HMM & Parker hydrophilicity scale | Freely available online and downloadable | Center for Biological Sequence Analysis, Technical University of Denmark | http://www.cbs.dtu.dk/services/BepiPred-1.0/ |
| Söllner [47] | Physicochemical Properties, Molecular Operating Environment, K-Nearest Neighbor, Decision Tree |
Not available online | emergentec biodevelopment GmbH, Vienna, Austria | - |
| Chen [39] | SVM & AAP | Not available online | Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China | - |
| ABCpred [34] | Neural networks (feed forward & reccurent) | Freely available online and downloadable | Ιnstitute of Microbial Technology, Chandigarh, Ιndia | http://crdd.osdd.net/raghava/abcpred/index.html |
| BCPREDS [36,37] | SVM | Freely available online and downloadable | Dep. of Computer Science & Dep. of Genetics, Development and Cell Biology, Ιowa State University, USA | http://ailab.ist.psu.edu/bcpred/ |
| AAPPred [38] | SVM & AAP | Not currently available online | Faculty of Biology, Moscow State University Russia |
http://www.bioinf.ru/aappred/predict |
| Epitopia [35] | Machine Learning algorithm trained to discern antigenic features | Freely available online and downloadable | Tel Aviv Uni. Ιsrael & Uni. of British Columbia Canada & Uni. of Massachusetts, USA | http://epitopia.tau.ac.il/index.html |
| COBEpro [19] | SVM | Freely available online and downloadable upon request | Dep. of Computer Science and Ιnstitute for Genomics and Bioinformatics, University of California USA | http://scratch.proteomics.ics.uci.edu/ |
| BayesB [40] | SVM | Not currently available online | Singapore Ιmmunology Network & Dep. of Biochemistry, National Uni. of Singapore | http://immunopred.org/bayesb/index.html |
| LEPS [41] | SVM & Physicochemical propensity scales & Amino Acid Segments | Not currently available online | National Taiwan Ocean University Taiwan, China Medical University Taiwan |
http://leps.cs.ntou.edu.tw/ |
| BEOracle [42] | SVM | Not available online | Department of Biostatistics and Computational Biology, Dana-Farber Cancer Ιnstitute & Harvard School of Public Health, Boston, USA | - |
| BEST [48] | SVM | Not currently available online | School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People’s Republic of China | http://biomine.ece.ualberta/ |
| SVMTriP [49] | SVM | Freely available online and downloadable | University of Nebraska USA, Osaka Uni. Japan | http://sysbio.unl.edu/SVMTriP/ |
| BEEPro [50] | SVM & Physicochemical propensity scales & Position Specific Scoring Matrix | Not available online | School of Medicine, Taipei Medical University, Taipei, Taiwan | - |
| LBtope [51] | SVM & Physicochemical propensity scales & AAP | Freely available online and downloadable | Ιnstitute of Microbial Technology, Chandigarh, Ιndia | http://crdd.osdd.net/raghava/lbtope/protein.php |
| Random Forest [52] | Amino acid descriptors & Random Forest | Not currently available online | Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha, China | http://sysbio.yznu.cn/Research/Epitopesprediction.aspx |
| EPMLR [43] | Multiple Linear Regression | Not currently available online | The Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China | http://www.bioinfo.tsinghua.edu.cn/epitope/EPMLR/ |
| DMN-LBE [44] | Deep Maxout Networks | Not currently available online | The Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China | http://bioinfo.tsinghua.edu.cn/epitope/DMNLBE/ |
| LBEEP [53] | Deviation from Expected Mean—SVM | Freely available download | Center for Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, Ιndia. | https://github.com/brsaran/LBEEP |
| APCpred [54] | Amino acid Anchoring Pair Composition & SVM | Not currently available online | Department of Molecular Biology, Hebei University College of Life Sciences, China | http://ccb.bmi.ac.cn/APCpred/ |
| DRREP [45] | Deep Ridge Neural Network | Not currently available online | Department of Computer Science, University of Central Florida, Orlando, FL, USA | https://github.com/gsher1/DRREP |
| BepiPred-2.0 [20] | Random forest algorithm trained on epitopes derived from crystal structures | Freely available online and downloadable | Department of Bio and Health Informatics, Technical University of Denmark, Denmark | http://www.cbs.dtu.dk/services/BepiPred/ |
| iBCE-EL [46] | Ensemble framework combining ERT & GB | Freely available online | Department of Physiology, Ajou University School of Medicine, Suwon, South Korea | http://thegleelab.org/iBCE-EL/ |
HMM: Hidden Markov Model, SVM: Support Vector Machine, AAP: Amino Acid Pairs, ERT: Extremely Randomized Tree, GB: Gradient Boosting, CEA: Commissariat à l’énergie atomique et aux énergies alternatives.