AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes

Abstract

AlgPred 2.0 is a web server developed for predicting allergenic proteins and allergenic regions in a protein. It is an updated version of AlgPred developed in 2006. The dataset used for training, testing and validation consists of 10 075 allergens and 10 075 non-allergens. In addition, 10 451 experimentally validated immunoglobulin E (IgE) epitopes were used to identify antigenic regions in a protein. All models were trained on 80% of data called training dataset, and the performance of models was evaluated using 5-fold cross-validation technique. The performance of the final model trained on the training dataset was evaluated on 20% of data called validation dataset; no two proteins in any two sets have more than 40% similarity. First, a Basic Local Alignment Search Tool (BLAST) search has been performed against the dataset, and allergens were predicted based on the level of similarity with known allergens. Second, IgE epitopes obtained from the IEDB database were searched in the dataset to predict allergens based on their presence in a protein. Third, motif-based approaches like multiple EM for motif elicitation/motif alignment and search tool have been used to predict allergens. Fourth, allergen prediction models have been developed using a wide range of machine learning techniques. Finally, the ensemble approach has been used for predicting allergenic protein by combining prediction scores of different approaches. Our best model achieved maximum performance in terms of area under receiver operating characteristic curve 0.98 with Matthew’s correlation coefficient 0.85 on the validation dataset. A web server AlgPred 2.0 has been developed that allows the prediction of allergens, mapping of IgE epitope, motif search and BLAST search (https://webs.iiitd.edu.in/raghava/algpred2/).

Designing Multi-Antigen Vaccines Against Acinetobacter baumannii Using Systemic Approaches

“…Transmembrane helices were predicted with TMHMM 2.0 (41). Allergenicity was predicted by AllerTop 2.0 (42) and the five methods available in AlgPred 2.0 (43). Toxicity was predicted with ToxinPred (44) using the "SVM (Swiss-Prot) + Motif based" method.…”

ChAlPred: A Web Server for Prediction of Allergenicity of Chemical Compounds

“…Allergy is an inappropriate reaction of the immune response when it misidentifies a harmless foreign substance as a threat. 1 These foreign substances are known as allergens, which could trigger several allergic reactions and lead to various allergic diseases. Different types of aeroallergens (e.g., pollens, spores, dust mites), food allergens (e.g., eggs, peanuts, tree nuts, genetically modified foods), and chemical allergens in personal care products (e.g., fragrances in the skin and hair care products, dyes, creams) 1, 2, 3 can lead to allergic symptoms such as allergic asthma, rhinitis, skin reactions and anaphylaxis.…”

“…1 These foreign substances are known as allergens, which could trigger several allergic reactions and lead to various allergic diseases. Different types of aeroallergens (e.g., pollens, spores, dust mites), food allergens (e.g., eggs, peanuts, tree nuts, genetically modified foods), and chemical allergens in personal care products (e.g., fragrances in the skin and hair care products, dyes, creams) 1, 2, 3 can lead to allergic symptoms such as allergic asthma, rhinitis, skin reactions and anaphylaxis. 1, 4 Anaphylactic shock involves a series of allergic reactions from mild symptoms like itchy skin, rashes, facial swelling, irritation of the eyes leading to watery eyes and nose to severe symptoms like shortness of breath, lack of consciousness, weak pulse, nausea, vomiting, which can even lead to death if untreated.…”

“…There is a wide variety of molecules that can pose a threat as allergens including biological molecules like proteins and peptides or some chemical compounds. 1 In the past, several methods have been proposed to predict protein allergens from genetically engineered foods, vaccines and therapeutics. All the available methods are based on protein/peptide allergens, such as the recently developed method AlgPred 2.0.…”

“…All the available methods are based on protein/peptide allergens, such as the recently developed method AlgPred 2.0. 1, 12 Many other methods such as AllerTool 13 , AllerHunter 14 , AllerTOP 15 , AllerTOPv2 16 , PREAL 17 , AllergenFP 18 , AllerCatPro 2 are heavily used by the scientific community. These methods are especially used in clinical researcher for designing proteins with desired allergenicity.…”