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COBEpro: a novel system for predicting continuous B-cell epitopes.

ABSTRACT: Accurate prediction of B-cell epitopes has remained a challenging task in computational immunology despite several decades of research. Only 10% of the known B-cell epitopes are estimated to be continuous, yet they are often the targets of predictors because a solved tertiary structure is not required and they are integral to the development of peptide vaccines and engineering therapeutic proteins. In this article, we present COBEpro, a novel two-step system for predicting continuous B-cell epitopes. COBEpro is capable of assigning epitopic propensity scores to both standalone peptide fragments and residues within an antigen sequence. COBEpro first uses a support vector machine to make predictions on short peptide fragments within the query antigen sequence and then calculates an epitopic propensity score for each residue based on the fragment predictions. Secondary structure and solvent accessibility information (either predicted or exact) can be incorporated to improve performance. COBEpro achieved a cross-validated area under the curve (AUC) of the receiver operating characteristic up to 0.829 on the fragment epitopic propensity scoring task and an AUC up to 0.628 on the residue epitopic propensity scoring task. COBEpro is incorporated into the SCRATCH prediction suite at http://scratch.proteomics.ics.uci.edu.

SUBMITTER: Sweredoski MJ

PROVIDER: S-EPMC2644406 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

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COBEpro: a novel system for predicting continuous B-cell epitopes.

Sweredoski Michael J MJ Baldi Pierre P

Protein engineering, design & selection : PEDS 20081210 3

Accurate prediction of B-cell epitopes has remained a challenging task in computational immunology despite several decades of research. Only 10% of the known B-cell epitopes are estimated to be continuous, yet they are often the targets of predictors because a solved tertiary structure is not required and they are integral to the development of peptide vaccines and engineering therapeutic proteins. In this article, we present COBEpro, a novel two-step system for predicting continuous B-cell epit ...[more]

PMID: 19074155

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Project description:BACKGROUND:The application of peptide based diagnostics and therapeutics mimicking part of protein antigen is experiencing renewed interest. So far selection and design rationale for such peptides is usually driven by T-cell epitope prediction, available experimental and modelled 3D structure, B-cell epitope predictions such as hydrophilicity plots or experience. If no structure is available the rational selection of peptides for the production of functionally altering or neutralizing antibodies is practically impossible. Specifically if many alternative antigens are available the reduction of required synthesized peptides until one successful candidate is found is of central technical interest. We have investigated the integration of B-cell epitope prediction with the variability of antigen and the conservation of patterns for post-translational modification (PTM) prediction to improve over state of the art in the field. In particular the application of machine-learning methods shows promising results. RESULTS:We find that protein regions leading to the production of functionally altering antibodies are often characterized by a distinct increase in the cumulative sum of three presented parameters. Furthermore the concept to maximize antigenicity, minimize variability and minimize the likelihood of post-translational modification for the identification of relevant sites leads to biologically interesting observations. Primarily, for about 50% of antigen the approach works well with individual area under the ROC curve (AROC) values of at least 0.65. On the other hand a significant portion reveals equivalently low AROC values of < or = 0.35 indicating an overall non-Gaussian distribution. While about a third of 57 antigens are seemingly intangible by our approach our results suggest the existence of at least two distinct classes of bioinformatically detectable epitopes which should be predicted separately. As a side effect of our study we present a hand curated dataset for the validation of protectivity classification. Based on this dataset machine-learning methods further improve predictive power to a class separation in an equilibrated dataset of up to 83%. CONCLUSION:We present a computational method to automatically select and rank peptides for the stimulation of potentially protective or otherwise functionally altering antibodies. It can be shown that integration of variability, post-translational modification pattern conservation and B-cell antigenicity improve rational selection over random guessing. Probably more important, we find that for about 50% of antigen the approach works substantially better than for the overall dataset of 57 proteins. Essentially as a side effect our method optimizes for presumably best applicable peptides as they tend to be likely unmodified and as invariable as possible which is answering needs in diagnosis and treatment of pathogen infection. In addition we show the potential for further improvement by the application of machine-learning methods, in particular Random Forests.

Dataset Information

COBEpro: a novel system for predicting continuous B-cell epitopes.

Publications

COBEpro: a novel system for predicting continuous B-cell epitopes.

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