3D images of the results from Intersection and Union of PepMapper.

<p>The candidate epitopes of 3IU3 are shown in the shape of spacefill and cpk color format with the rest amino acids in backbone. The image on the top is the result from <i>Intersection</i> of PepMapper whereas the bottom one is the result from <i>Union</i> of PepMapper. It can be clearly seen on these images that <i>Intersection</i> provides more confined prediction as most of the residues lie on the interface whereas <i>Union</i> outlines a larger area that may cover (part of) the potential epitopic region.</p

Test cases for validation and assessment.

#<p>Number of peptides × peptide length.</p>*<p>1N8Z^* shares the same crystal complex with 1N8Z in PDB database.</p

Statistical results of PepMapper.

*<p>Inter stands for intersection of the results; Union stands for union of the results.</p

An example of text presentation of Intersection and Union of PepMapper.

<p>Results of <i>Intersection</i> and <i>Union</i> are listed in text. The overlapped candidate peptides of 1JRH are highlighted in yellow in the two boxes.</p

Statistical results of Pep-3D-Search and MimoPro.

<p>TP: number of true positive; PE: number of predicted epitope; Se: sensitivity; Sp: specificity; Pr: precision.</p

Flow chart of PepMapper.

<p>Solid lines indicate the process sequences of PepMapper whereas dashed lines are for that of either MimoPro or Pep-3D-Search alone.</p

Inhibition of AVFluIgG01 on HA-mediated cell-cell fusion.

<p>A. AVFluIgG01 inhibits the low-pH induced cell-cell fusion in Vero cells that were transfected with the plasmid encoding Viet04 HA protein (pViet04-HA). The cells were stained with crystal violet. (a) Control cells (no HA transfection); (b) Positive control (without antibodies); (c) Treated with 50 µg/ml AVFluIgG01; (d) Treated with 50 µg/ml control mAb (AVFluIgG03). <b>B</b>. AVFluIgG01 inhibits cell fusion between 293T effector cells and MDCK target cells at a dose-dependent manner. 293T cells were co-transfected with pViet04-HA and pGAL4-VP16 and MDCK cells were transfected with pGal5-luc. After fusion induced by low-pH, the luciferase activity was measured in the cell lysates. The percent inhibition and IC₅₀ were calculated.</p

Reactivity of AVFluIgG01 with different HA antigens.

<p><b>A</b>. Representative sequences of synthesized HA peptides (Viet04). <b>B</b>. Reactivity of AVFluIgG01 with the recombinant HA or HA1 proteins (Viet04) and overlapping peptides in ELISA. <b>C</b>. Reactivity of AVFluIgG01 with the native and reduced HA proteins (HK06) in ELISA. Synthesized peptides at 5 µg/ml or recombinant HA proteins at 1 µg/ml were used to coat 96-well microtiter plates, and AVFluIgG01 or a control mAb was tested at a final concentration of 10 µg/ml.</p

Prediction of AVFluIgG01 epitope by minotopes.

<p><b>A</b>. Affinity-selected minotopes from a random peptide phage display library. The selection frequency of a specific minotope is shown in parentheses. <b>B</b>. Predicted amino acid residues by Mapitope. <b>C</b>. Predicted amino acid residues by Pep-3D-Search. The common residues that are predicted by both algorithms are underlined and shown in bold.</p

Inhibition of AVFluIgG01 on the pH-induced conformational changes of HA.

<p>The recombinant Viet04 HA proteins were incubated with or without AVFluIgG01 (<b>A</b>) or its Fab (<b>B</b>) at 37°C for 1 h. The mixture was either held at pH 7.5 (lanes 2, 4, 6 and 8) or changed to pH 5.0 (lanes 1, 3, 5 and 7) at 37°C for 1 h. After the pH was restored to 7.5, trypsin (1 µg/ml) was added to detect the acquisition of pH-induced protease susceptibility (lanes 5 to 8). The samples were then analyzed by western blotting. Molecular markers are given on the left.</p