In Silico Comparative Analysis of Predicted B Cell Epitopes against Dengue Virus (Serotypes 1–4) Isolated from the Philippines
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design
2.2. Protocols and Equipment
2.2.1. Collection of DENV Nucleotide Sequences
2.2.2. Prediction and Documentation of B-Cell and T-Cell Epitopes
2.3. Data Visualization and Analyses
3. Results
3.1. Prediction of B Cell Epitopes
3.1.1. DENV-1
3.1.2. DENV-2
3.1.3. DENV-3
3.1.4. DENV-4
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Position | Peptide Sequence | Antigenicity (mean) | Surface Accessibility (mean) | Hydrophilicity (mean) | Frequency (n = 10) | Rank According to Antigenicity | |
---|---|---|---|---|---|---|---|
Start | End | ||||||
242 | 251 | TAHAKKQEVV | 1.063 | 2.93 | 1.5561 | 10 | 1 |
321 | 330 | LVQVKYEGTD | 1.062 | 2.19 | 1.1965 | 10 | 2 |
141 | 150 | VTVHTGDQHQ | 1.056 | 3.49 | 1.2373 | 10 | 3 |
142 | 151 | TVHTGDQHQV | 1.056 | 3.49 | 1.2373 | 10 | 4 |
290 | 299 | DKLTLKGVSY | 1.056 | 1.48 | 1.188 | 10 | 5 |
Position | Peptide Sequence | Antigenicity (mean) | Surface Accessibility (mean) | Hydrophilicity (mean) | Frequency (n = 10) | Rank According to Antigenicity | |
---|---|---|---|---|---|---|---|
Start | End | ||||||
243 | 252 | PHAKKQDVVV | 1.112 | 1.158 | 2.26 | 10 | 1 |
86 | 95 | QDKRVVCKHS | 1.091 | 1.395 | 3.42 | 1 | 2 |
85 | 94 | EQDKRVVCKH | 1.075 | 1.803 | 3.55 | 1 | 3 |
51 | 60 | KHPATLRKYC | 1.07 | 1.916 | 1.74 | 8 | 4 |
128 | 137 | KVVQPENLEY | 1.066 | 2.116 | 1.79 | 6 | 5 |
129 | 138 | VVQPENLEYT | 1.064 | 1.527 | 1.74 | 6 | 6 |
86 | 95 | QDKRFVCKHS | 1.062 | 1.641 | 2.87 | 9 | 7 |
51 | 60 | KQPATLRKYC | 1.061 | 2.453 | 2.13 | 2 | 8 |
356 | 365 | PIVTEKDSPV | 1.061 | 1.193 | 2.4 | 4 | 9 |
55 | 64 | TLRKYCIEAK | 1.053 | 1.113 | 1.3 | 3 | 10 |
Position | Peptide Sequence | Antigenicity (mean) | Surface Accessibility (mean) | Hydrophilicity (mean) | Frequency (n = 10) | Rank According to Antigenicity | |
---|---|---|---|---|---|---|---|
Start | End | ||||||
90 | 99 | YVCKHTYVDR | 1.118 | 1.048 | 1.74 | 10 | 1 |
354 | 363 | PVVSKKEEPV | 1.085 | 1.763 | 2.66 | 1 | 2 |
128 | 137 | KVVQHENLKY | 1.078 | 2.102 | 1.58 | 9 | 3 |
129 | 138 | VVQHENLKYT | 1.076 | 1.517 | 1.53 | 9 | 4 |
130 | 139 | VQHENLKYTV | 1.076 | 1.517 | 1.53 | 9 | 5 |
131 | 140 | QHENLKYTVV | 1.076 | 1.508 | 1.53 | 1 | 6 |
354 | 363 | PVVTKKEEPV | 1.075 | 1.907 | 2.53 | 8 | 7 |
87 | 96 | DQNYVCKHTY | 1.072 | 2.023 | 2.99 | 1 | 8 |
86 | 95 | QDQNYVCKHT | 1.057 | 2.235 | 3.78 | 1 | 9 |
142 | 151 | TVHTGDQHQV | 1.056 | 1.194 | 3.49 | 1 | 10 |
Position | Peptide Sequence | Antigenicity (mean) | Surface Accessibility (mean) | Hydrophilicity (mean) | Frequency (n = 10) | Rank According to Antigenicity | |
---|---|---|---|---|---|---|---|
Start | End | ||||||
169 | 178 | PSVEVKLPDY | 1.096 | 1.558 | 1.57 | 8 | 1 |
166 | 175 | PRSPSVEVKL | 1.082 | 1.559 | 1.83 | 10 | 2 |
167 | 176 | RSPSVEVKLP | 1.082 | 1.559 | 1.83 | 10 | 3 |
366 | 375 | QHGTTVVKVK | 1.082 | 1.001 | 2.45 | 1 | 4 |
168 | 177 | SPSVEVKLPD | 1.081 | 1.332 | 2.41 | 8 | 5 |
166 | 177 | SPSVEVKLPE | 1.08 | 1.366 | 2.19 | 2 | 6 |
244 | 253 | HAKRQDVTVL | 1.078 | 1.193 | 1.87 | 9 | 7 |
170 | 179 | SVEVKLPEYG | 1.076 | 1.022 | 1.71 | 2 | 8 |
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Abesamis, L.M.I.; Aliping, E.G.A.; Armada, F.K.G.H.; Danao, M.F.; del Valle, P.D.B.; Regencia, Z.J.G.; Baja, E.S.; Ligsay, A.D. In Silico Comparative Analysis of Predicted B Cell Epitopes against Dengue Virus (Serotypes 1–4) Isolated from the Philippines. Vaccines 2022, 10, 1259. https://doi.org/10.3390/vaccines10081259
Abesamis LMI, Aliping EGA, Armada FKGH, Danao MF, del Valle PDB, Regencia ZJG, Baja ES, Ligsay AD. In Silico Comparative Analysis of Predicted B Cell Epitopes against Dengue Virus (Serotypes 1–4) Isolated from the Philippines. Vaccines. 2022; 10(8):1259. https://doi.org/10.3390/vaccines10081259
Chicago/Turabian StyleAbesamis, Lyn Marielle I., Evan Gilles A. Aliping, Fritz Khrystian Gabriel H. Armada, Mirriam F. Danao, Pamela Denise B. del Valle, Zypher Jude G. Regencia, Emmanuel S. Baja, and Antonio D. Ligsay. 2022. "In Silico Comparative Analysis of Predicted B Cell Epitopes against Dengue Virus (Serotypes 1–4) Isolated from the Philippines" Vaccines 10, no. 8: 1259. https://doi.org/10.3390/vaccines10081259