In past number of databases (e.g. MHCPEP, MHCBN, AntijenDB, IEDB, BCIPEP, IMGT) have been developed to assists the researchers working in the field of adaptive immunity. Best of authorís knowledge no method have been developed in the field of innate immunity. Innate immune system has long been thought of just as the first line of defense whose only function is to contain the infection until the real player i.e. cells of adaptive immune response ready for defense. Recently, it has been demonstrated in number studies that the innate immune system does not merely acts as the first line of defense but provides critical signals for the development of specific adaptive immune response. In order to assist scientific community, we collected and compiled information related to innate immunity from literature and public databases (e.g. Swiss-Prot, TrEMBL).
Pattern-recognition receptors are germ-line encoded receptors, employed by the innate immune system to recognize evolutionarily conserved patterns from pathogens called Pathogen Associated Molecular Patterns (PAMPs). These receptors are necessary for guiding adaptive immune system for generating appropriate response against any pathogen. A database PRRDB has been developed that provides extensive information pattern recognizing receptors (PRRs) and their ligands. It contains around 500 PRRs sequences belonging to 77 distinct organisms ranging from insects to humans (See Figure 1). This includes 177 Toll-like receptors, 124 are Scavenger receptors, 20 are mannose receptors, 41 are C-type lectin like domain containing receptors, 17 are DC-SIGN, 43 are Peptidoglycan recognition receptors and 67 are Nucleotide Binding Site-Leucine repeats rich receptors. These receptors have been also classified as single-pass type I/II membrane proteins, multi-pass membrane protein, cytoplasmic or secreted proteins depending upon their site of expression. The database also provides information about 228 PRR ligands (79 endogenous and 149 exogenous). The database covers wide range of ligands including carbohydrates, proteins, nucleic acids, glycolipids, glycoproteins, lipopeptides. PRRDB also provides a number of online web tools that allow users to retrieve information and analyze data. It includes keyword search and browsing of PRRs and ligands, similarity search against PRRs. It provides external links to number of databases including Swiss-Prot and Pubmed. This databases is available for academic community via internet from URL http://www.imtech.res.in/raghava/prrdb/.
Murine models of immune processes and immunological diseases14
Resource of Asian Primary Immunodeficiency Diseases
The GPX Macrophage Expression Atlas (GPX-MEA) is an online resource for expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. GPX Macrophage Expression Atlas (GPX-MEA) follows the MIAME standard and includes an objective quality score with each experiment. It places special emphasis on rigorously capturing the experimental design and enables the statistical analysis of expression data from different micro-array experiments. Studies may be queried on the basis of experimental parameters, sample information and quality assessment score. The ability to compare the expression values of individual genes across multiple experiments is provided. In addition, the database offers access to experimental annotation and analysis files and includes experiments and raw data previously unavailable to the public. This is the first example of a focussed macrophage gene expression database that allows efficient identification of transcriptional patterns which provide novel insights into biology of this cell system. GPX-MEA is available through the GPX website at (http://www.gti.ed.ac.uk/GPX).
This work was supported by the Scottish Higher Education Funding Council, Biotechnology and Biological Sciences Research Council, Wellcome Trust and the European Regional Development Fund. We thank our colleagues at the GTI and collaborators Liu Bin, Ke Shuai, Reinhard Hoffmann, Xiaoyu Hu, Rachael ZoŽ Murray, Jenny Stow, Thomas Nutman, Damien Chaussabel, Daniel Popkin, Skip Virgin and Ioannis Tassiulas for contributing to this resource.
Vaccine Investigation and Online Information Network
A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.
The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools.
NetNHC-3.0 is a web server for the prediction of human, mouse or monkey MHC Class I-peptide binding. Predictions are made for peptides of 8-11 amino acid length using artificial neural networks and weight matrices.
Protein Sequence Variability (PVS) is a web server for the prediction of conserved T-cell epitopes. Several variability metrics are used to compute the absolute site variability in multiple protein sequence alignments.
SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.
The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI s Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.
PredBALB/c is a tool that will predict MHC binding peptides in your protein sequence of interest for the H2d haplotype of the BALB/c mouse.
Major Histocompatibility Complex Predictor (MHCPred) predicts the binding affinities of major histocompatibility complexes to ligands.
DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.
AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.