20 research outputs found

    Length distribution of amino terminal PFRs for MHC-II binding and non-binding peptides

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    <p><b>Copyright information:</b></p><p>Taken from "Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method"</p><p>http://www.biomedcentral.com/1471-2105/8/238</p><p>BMC Bioinformatics 2007;8():238-238.</p><p>Published online 4 Jul 2007</p><p>PMCID:PMC1939856.</p><p></p> All peptide data for the three alleles in the AntiJen and IEDB data sets are included in the figure. Binding peptides have an affinity stronger than 500 nM. The PFR is defined as the residues flanking the peptide-binding core as determined by the SMM-align method

    Illustration of benchmark redefinition on Lysozyme.

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    <p>6 unique discontinuous epitopes have been identified for lysozyme. Including this comprehensive information on multiple epitopes for Lysozyme, the reported performance is increased. Predictions are illustrated as a heatmap on the protein surface where Red = high prediction score, Blue = low prediction score.</p

    Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking

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    <div><p>The interaction between antibodies and antigens is one of the most important immune system mechanisms for clearing infectious organisms from the host. Antibodies bind to antigens at sites referred to as B-cell epitopes. Identification of the exact location of B-cell epitopes is essential in several biomedical applications such as; rational vaccine design, development of disease diagnostics and immunotherapeutics. However, experimental mapping of epitopes is resource intensive making <em>in silico</em> methods an appealing complementary approach. To date, the reported performance of methods for <em>in silico</em> mapping of B-cell epitopes has been moderate. Several issues regarding the evaluation data sets may however have led to the performance values being underestimated: Rarely, all potential epitopes have been mapped on an antigen, and antibodies are generally raised against the antigen in a given biological context not against the antigen monomer. Improper dealing with these aspects leads to many artificial false positive predictions and hence to incorrect low performance values. To demonstrate the impact of proper benchmark definitions, we here present an updated version of the <em>DiscoTope</em> method incorporating a novel spatial neighborhood definition and half-sphere exposure as surface measure. Compared to other state-of-the-art prediction methods, <em>Discotope-2.0</em> displayed improved performance both in cross-validation and in independent evaluations. Using <em>DiscoTope-2.0</em>, we assessed the impact on performance when using proper benchmark definitions. For 13 proteins in the training data set where sufficient biological information was available to make a proper benchmark redefinition, the average AUC performance was improved from 0.791 to 0.824. Similarly, the average AUC performance on an independent evaluation data set improved from 0.712 to 0.727. Our results thus demonstrate that given proper benchmark definitions, B-cell epitope prediction methods achieve highly significant predictive performances suggesting these tools to be a powerful asset in rational epitope discovery. The updated version of <em>DiscoTope</em> is available at <a href="http://www.cbs.dtu.dk/services/DiscoTope-2.0">www.cbs.dtu.dk/services/DiscoTope-2.0</a>.</p> </div

    Enhance prediction accuracy by inclusion of structural data of the biological unit.

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    <p>Illustration of prediction for KvAP potassium channel. Left: using only one antigen chain, middle: using the biological tetramer, right: Excluding membrane and cytoplasmic residues. Predictions are illustrated as a heatmap on the protein surface where Red = high prediction score, Blue = low prediction score. Note, that the stated performances are for the PDB entry 1K4C and not the complete potassium homology group.</p

    Predictive positive value (PPV) and sensitivity for <i>DiscoTope-2.0</i>, <i>DiscoTope-1.2</i>, <i>PEPITO</i> and <i>ElliPro</i> on the evaluation data set.

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    <p># Residues gives the number of highest scoring prediction included for each antigen, PPV gives the predictive positive value (true positives)/(predicted positives)), and Sens gives the sensitivity (true positives)/(actual positives)).</p

    Predictions for Gp120 plotted on the protein structure including bound antibody.

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    <p>Each residue in the structure is colored from blue to red according to its <i>DiscoTope-2.0</i> score. Blue indicates low scores (predicted to be non-epitope residue) and red indicates high scores (predicted to be epitope residue). Yellow indicates possible glycosylation sites retrieved from UNIPROT accession number P04578 (<a href="http://www.uniprot.org" target="_blank">www.uniprot.org</a>). a) Gp120 surface representation and antibody cartoon representation. b) Gp120 and antibody cartoon representation. Note, the red alpha-1 helix, which is normally buried in the inner domain of Gp120 involved in Gp41∶Gp120 complex formation, is exposed in the crystal structure.</p

    Cross-validated performance.

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    <p>Performances of different methods for predicting B-cell epitopes evaluated on the DiscoTope dataset. From left to right: The original <i>DiscoTope</i> method, the uncombined log-odds ratio scores as described in text, the surface measures; UHS, RSA, FS HSE and Ta (see text) and the <i>DiscoTope2.0</i> method as described in text. Performance of the original <i>DiscoTope</i> method was obtained from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002829#pcbi.1002829-Andersen1" target="_blank">[12]</a>.</p

    Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction-1

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    <p><b>Copyright information:</b></p><p>Taken from "Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction"</p><p>http://www.biomedcentral.com/1471-2105/8/424</p><p>BMC Bioinformatics 2007;8():424-424.</p><p>Published online 31 Oct 2007</p><p>PMCID:PMC2194739.</p><p></p>ng NetCTL-1.2 is compared to the rank assigned when using the test method (EpiJen, MAPPP, MHC-pathway, or WAPP). The height of the bars indicates how often, respectively, NetCTL or the test method ranks the epitope highest. The HIV dataset has been used for the analysis. When comparing NetCTL-1.2 to either of the test methods, only predictions for supertypes that the test method covers are included. The HIVdataset has been used for the analysis. ** The difference is significant at P < 0.01. * The difference is significant at P < 0.05

    Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction-2

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    <p><b>Copyright information:</b></p><p>Taken from "Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction"</p><p>http://www.biomedcentral.com/1471-2105/8/424</p><p>BMC Bioinformatics 2007;8():424-424.</p><p>Published online 31 Oct 2007</p><p>PMCID:PMC2194739.</p><p></p>tricted to as many supertypes as possible, NetCTL-1.2 is compared to each of the other methods separately. For each comparison, only predictions for supertypes that the test method covers are included. The average specificity is found at a predefined average sensitivity using either NetCTL-1.2 or one of the four test methods (EpiJen, MAPPP, MHC-pathway, WAPP). Average sensitivity = 0.3, Average sensitivity = 0.5, Average sensitivity = 0.8. Only NetCTL-1.2, MAPPP and MHC-pathway provide enough predicted scores to obtain a sensitivity of 0.8. The error bars are the standard error. ** The difference is significant at P < 0.01. * The difference is significant at P < 0.05
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