Sequence-based B-cell epitope detection software tools | Immune system data analysis
For over 30 years, computational methods have been developed for facilitating epitope recognition. In the past, the majority of the in silico methods were focused on linear epitopes. Most of these approaches are sequence-based and use amino acid-based propensity scales, such as hydrophilicity, solvent accessibility, secondary structure and flexibility; a score derived from the propensity scales is assigned to each residue, and the whole sequence is examined for high-scoring window fragments, which are then predicted as epitopes.
Predicts the location of linear B-cell epitopes using a combination of a hidden Markov model (HMM) and a propensity scale method. BepiPred is a web server constructed from a large set of structurally defined B cell epitopes. The interface can aid researchers with limited computational knowledge to use and understand the results to their full extent. Additionally, the advanced option allows more experienced researchers to further interpret the output based on additionally predicted structural features.
Prediction of linear B-cell epitopes, using physico-chemical properties. Bcepred is able to predict epitopes with 58.7% accuracy using Flexibility, Hydrophobicity, Polarity, and Surface properties combined at a threshold of 2.38.
Provides users a support vector machines (SVM) prediction model using Bayes Feature Extraction (BFE) to predict linear B-cell epitopes of diverse lengths (12- to 20-mers). Bayesb is based on the report that linear B-cell epitopes and non-epitope sequences have distinctive residue composition and position-specific propensity patterns which could be used for epitope discrimination in silico. It aims to discriminating epitopes from non-epitopes in benchmark datasets and annotated antigenic proteins.
The identification and characterization of B-cell epitopes play an important role in vaccine design, immunodiagnostic tests, and antibody production. BCPREDS is a method for predicting linear B-cell epitopes using the subsequence kernel.
Offers a platform for comprehensive analyses of B cell receptor repertoires, using IMGT/HighV-QUEST formatted data. bcRep is a R package that combines techniques for studying clones and also the total set of input sequences or subsets of sequences. This program allows users to filter these sequences for their functionality or junction frame usage, and clones also for their size.