OSCAR-star

Optimized Side Chain Atomic eneRgy (OSCAR)-star based on orientation-dependent energy functions and a rigid rotamer model.Availability: OSCAR-star and the 218 test proteins are available for download at http://sysimm.ifrec.osaka-u.ac.jp/OSCARContact: pj.ca.u-akaso.cerfi@yeldnatsSupplementary information: Supplementary data are available at Bioinformatics online.</p

List of the protein binding site prediction methods and their obtained AUC results.

a<p>Conserved residues are selected as for common binding site prediction.</p

ROC curves for AAP, BCPred, and SVMTriP.

<p>ROC curves for AAP, BCPred, and SVMTriP.</p

List of the conformational B-cell epitope prediction methods and their obtained AUC results.

a<p>The AUC value is obtained from the Reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062249#pone.0062249-Zhang1" target="_blank">[23]</a>.</p>b<p>10% of surface residues are returned as predicted epitopic residues.</p>c<p>Estimated based on the Figure 4 in the Reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062249#pone.0062249-Zhang1" target="_blank">[23]</a>.</p

Weights of tri-peptides in the optimal SVM model.

*<p>Weight scores are calculated by the formula w = ∑ α_i<i>x_i</i>. Here α is dual representation of the decision boundary; and <i>x_i</i> (i = 0, 1, 2…n) is vector described in SVM model. Both α_i and <i>x_i</i> are available in model file.</p

Comparison among the tri-peptide subsequence models with or without propensity.

*<p>The corresponding model is defined as SVMTriP.</p

Performance of different linear B-cell epitope prediction methods.

*<p>The results for AAP <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045152#pone.0045152-Chen1" target="_blank">[14]</a> and BCPred <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045152#pone.0045152-ElManzalawy1" target="_blank">[15]</a>, are obtained by the software implemented locally.</p

Tendency test for BCPred, AAP, and SVMTriP.

<p>Three bars at the same point on the x-axis are the results for APP (blue), BCPred (green), and SVMTriP (red), respectively. In the same bar, the light part is for the number of returned human peptide, and the dark part is for virus. For example, at the point of 400 returned peptides, the dark part in the red bar is 362, which means that 362 viral peptides are return in all 400 peptides by SVMTriP, and the light red part represents 38 human peptides.</p

Performance of SVMTriP models with different epitope lengths.

<p>Performance of SVMTriP models with different epitope lengths.</p