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The <t>3D</t> structure representation (top) of the molecular docking analysis of top-ranked MHC class <t>II</t> <t>epitopes</t> from different structural proteins (HA, NP, NA, and M2) of H5N1 clade 2.3.4.4b with chicken alleles BLB1 and BLB2 using the HADdock analysis server, ( A ) HA: RNVVWLIKKNDAYPT, ( B ) NP: EIEDLIFLARSALIL, ( C ) NA: FKYGNGVWIGRTKS, ( D ) M2: VYRRLKYGLKGGPST, and their respective interaction residues (bottom) obtained from the PDBsum database.
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The <t>3D</t> structure representation (top) of the molecular docking analysis of top-ranked MHC class <t>II</t> <t>epitopes</t> from different structural proteins (HA, NP, NA, and M2) of H5N1 clade 2.3.4.4b with chicken alleles BLB1 and BLB2 using the HADdock analysis server, ( A ) HA: RNVVWLIKKNDAYPT, ( B ) NP: EIEDLIFLARSALIL, ( C ) NA: FKYGNGVWIGRTKS, ( D ) M2: VYRRLKYGLKGGPST, and their respective interaction residues (bottom) obtained from the PDBsum database.
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The <t>3D</t> structure representation (top) of the molecular docking analysis of top-ranked MHC class <t>II</t> <t>epitopes</t> from different structural proteins (HA, NP, NA, and M2) of H5N1 clade 2.3.4.4b with chicken alleles BLB1 and BLB2 using the HADdock analysis server, ( A ) HA: RNVVWLIKKNDAYPT, ( B ) NP: EIEDLIFLARSALIL, ( C ) NA: FKYGNGVWIGRTKS, ( D ) M2: VYRRLKYGLKGGPST, and their respective interaction residues (bottom) obtained from the PDBsum database.
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The 3D structure representation (top) of the molecular docking analysis of top-ranked MHC class II epitopes from different structural proteins (HA, NP, NA, and M2) of H5N1 clade 2.3.4.4b with chicken alleles BLB1 and BLB2 using the HADdock analysis server, ( A ) HA: RNVVWLIKKNDAYPT, ( B ) NP: EIEDLIFLARSALIL, ( C ) NA: FKYGNGVWIGRTKS, ( D ) M2: VYRRLKYGLKGGPST, and their respective interaction residues (bottom) obtained from the PDBsum database.

Journal: Viruses

Article Title: A Pan-H5N1 Multiepitope DNA Vaccine Construct Targeting Some Key Proteins of the Clade 2.3.4.4b Using AI-Assisted Epitope Mapping and Molecular Docking

doi: 10.3390/v17091152

Figure Lengend Snippet: The 3D structure representation (top) of the molecular docking analysis of top-ranked MHC class II epitopes from different structural proteins (HA, NP, NA, and M2) of H5N1 clade 2.3.4.4b with chicken alleles BLB1 and BLB2 using the HADdock analysis server, ( A ) HA: RNVVWLIKKNDAYPT, ( B ) NP: EIEDLIFLARSALIL, ( C ) NA: FKYGNGVWIGRTKS, ( D ) M2: VYRRLKYGLKGGPST, and their respective interaction residues (bottom) obtained from the PDBsum database.

Article Snippet: To preserve the native-like conformation of conformational epitopes in the MEV, we used flexible linkers (GPGPG and EAAAK), performed 3D structure prediction with AlphaFold2 and Biovia Discovery Studio, and verified the model using energy minimization, Ramachandran analysis, and surface epitope mapping.

Techniques:

Structural analysis of the final multiepitope vaccine construct against H5N1 clade 2.3.4.4b: ( A ) shows the multiepitope vaccine construct’s topology diagram to visualize the secondary structure elements’ arrangements. The PDB files of the vaccine construct were provided as input for the PDBsum server; the results showed the cylinders, arrows, and lines, which represent the alpha-helix and beta strands, and the lines explain the connection via loops and chains. ( B ) The secondary structure prediction exactly matches the topology diagram, allowing the identification of the flexible regions, surface exposure, and potential antigenic sites; ( C ) shows the 3D structure of the vaccine construct modeled through Biovia Discovery Studio using the template sequence alignment method, and its corresponding Ramachandran plot ( D ) confirms the stability, with a greater number of blue dots on the respective region, confirms the quality of protein conformations, and ensures its accuracy.

Journal: Viruses

Article Title: A Pan-H5N1 Multiepitope DNA Vaccine Construct Targeting Some Key Proteins of the Clade 2.3.4.4b Using AI-Assisted Epitope Mapping and Molecular Docking

doi: 10.3390/v17091152

Figure Lengend Snippet: Structural analysis of the final multiepitope vaccine construct against H5N1 clade 2.3.4.4b: ( A ) shows the multiepitope vaccine construct’s topology diagram to visualize the secondary structure elements’ arrangements. The PDB files of the vaccine construct were provided as input for the PDBsum server; the results showed the cylinders, arrows, and lines, which represent the alpha-helix and beta strands, and the lines explain the connection via loops and chains. ( B ) The secondary structure prediction exactly matches the topology diagram, allowing the identification of the flexible regions, surface exposure, and potential antigenic sites; ( C ) shows the 3D structure of the vaccine construct modeled through Biovia Discovery Studio using the template sequence alignment method, and its corresponding Ramachandran plot ( D ) confirms the stability, with a greater number of blue dots on the respective region, confirms the quality of protein conformations, and ensures its accuracy.

Article Snippet: To preserve the native-like conformation of conformational epitopes in the MEV, we used flexible linkers (GPGPG and EAAAK), performed 3D structure prediction with AlphaFold2 and Biovia Discovery Studio, and verified the model using energy minimization, Ramachandran analysis, and surface epitope mapping.

Techniques: Construct, Sequencing