1 - 7 of 7 results

RimmPort

Prepares National Institute of Allergy and Infectious Diseases (NIAID)-funded research study datasets in ImmPort for analysis in R. RImmPort comprises of three main components: (i) a specification of R classes that encapsulate study data, (ii) foundational methods to load data of a specific study and (iii) generic methods to slice and dice data across different dimensions in one or more studies. It supports open formalisms to ensure that ImmPort curated study datasets are seamlessly accessible and ready for analysis, thus enabling innovative bioinformatics research in immunology.

ImmPort / The immunology database and analysis portal

Provides an immunology database and analysis portal system. ImmPort is the archival repository and dissemination vehicle for clinical and molecular datasets created by research consortia funded by the National Institute of Allergy and Infectious Diseases Division of Allergy, Immunology, and Transplantation. With more than 100 datasets publicly available and hundreds of downloads per month, ImmPort is an important source for raw data and protocols from clinical trials, mechanistic studies, and novel methods for cellular and molecular measurements. To facilitate data transfer, templates for data representation and standard operating procedures have also been created and are also publicly available. ImmPort facilitates transparency and reproducibility in immunology research, serves as an important resource for education, and enables newly generated hypotheses and data-driven science.

Cross-React

Enables prediction of cross-reactivity between distantly related allergenic proteins using their X-ray or homology modeled structures in combination with epitope analysis. Cross-React uses a patch analysis, solvent accessible surface area of amino acids, and structural similarity between amino acids in the epitope region of a query allergen and allergens in the SDAP database. The search results are ranked based on the calculated Pearson correlation coefficient (PCC) between the amino acid composition in the query epitope and the accessible surface patches on the target allergens. Cross-React can be used as a predictive tool to assess protein allergenicity and cross-reactivity.

SDAP / Structural Database of Allergenic Proteins

A web server that provides rapid, cross-referenced access to the sequences, structures and IgE epitopes of allergenic proteins. SDAP contains information about the allergen name, source, sequence, structure, IgE epitopes and literature references and easy links to the major protein (PDB, SWISS-PROT/TrEMBL, PIR-ALN, NCBI Taxonomy Browser) and literature (PubMed, MEDLINE) on-line servers. The computational component in SDAP uses an original algorithm based on conserved properties of amino acid side chains to identify regions of known allergens similar to user supplied peptides or selected from the SDAP database of IgE epitopes. This and other bioinformatics tools can be used to rapidly determine potential cross-reactivities between allergens and to screen novel proteins for the presence of IgE epitopes they may share with known allergens.

AllerTool

Obsolete
A web server with essential tools for the assessment of predicted as well as published cross-reactivity patterns of allergens. AllerTool includes graphical representation of allergen cross-reactivity information; a local sequence comparison tool that displays information of known cross-reactive allergens; a sequence similarity search tool for assessment of cross-reactivity in accordance to FAO/WHO Codex alimentarius guidelines; and a method based on support vector machine (SVM).

AllerHunter

Obsolete
A cross-reactive allergen prediction program built on a combination of support vector machine (SVM) and pairwise sequence similarity. Cross-reactivity is based on similarity of proteins to allergens. However, not all proteins with similar sequence or structure to known allergens are cross-reactive allergens. AllerHunter aims to predict allergens and non-allergens with high sensitivity and specificity, without compromising efficiency at classification of proteins with similar sequence to known allergens.