Links to External Resources

Hyperlink Category
Public Databases, Prediction Algorithms, and Other Tools
Antibody Related Links
Bioinformatics Resource Centers
MHC and TCR Related Links
Protein Related Links
Laboratory Resources
Biodefense Resources

Public Databases, Prediction Algorithms, and Other Tools
TitleDescription
Immunoinformatics Server at UAMSThis server provides mirrors of a number of T and B cell epitope prediction tools and databases from the Raghava group.
AntiJenAntiJen v2.0 is a database containing quantitative binding data for peptides binding to MHC ligands, TCR-MHC complexes, T cell epitopes, TAP, B cell epitope molecules, and immunological protein-protein interactions. AntiJen includes a peptide library, copy numbers, and diffusion coefficient data. All entries are from published experimentally determined data. The database currently holds over 24,000 entries. No data in AntiJen is from prediction experiments.
MHCBN (MHC Binding and Non-Binding Peptides) MHCBN is a curated database consisting of detailed information about major histocompatibility complex (MHC) binding, non-binding peptides, and T-cell epitopes. Version 4.0 provides information about peptides interacting with TAP and MHC-linked autoimmune diseases.
ProPredThe aim of ProPred is to predict MHC Class-II binding regions in an antigen sequence, using quantitative matrices derived from published literature by Sturniolo, et al., 1999. The server will assist in locating promiscuous binding regions that are useful in selecting vaccine candidates.
PAProcPAProC is a public prediction tool for proteasomal cleavages, offering information on both the general cleavability of amino acid sequences (cuts per amino acids) and individual cleavages (positions and estimated strength).
BIMASBIMAS ranks potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature by Dr. Kenneth Parker, Applied Biosystems.
HIV Molecular Immunology Database (Los Alamos) Data included in this database is extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL, T helper, and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section.
MHCPEPMHCPEP is a database comprising over 13000 peptide sequences known to bind MHC molecules. Entries were compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions, and publication references.
EPIPREDICTThis software predicts HLA-class II restricted T cell epitopes and ligands. By means of synthetic combinatorial peptide libraries new concepts to describe peptide-HLA class II interaction in a quantitative way were developed. The binding contribution of every amino acid side chain in a class II-ligand is described by allele-specific two-dimensional databases.
NetChopNetChop produces neural network predictions for cleavage sites of the human proteasome. NetChop has been trained on human data only, and will therefore presumably have better performance for prediction of the cleavage sites of the human proteasome. However, since the proteasome structure is quite conserved, the server may produce reliable predictions for other mammalian proteasomes.
EPIMHCEPIMHC is a database of peptides that bind to MHC molecules.
Macaque MHC Prediction of peptide binding to Macaque MHC class-I molecules
ImmPortImmPort, the Immunology Database and Analysis Portal, is a one stop shop to access reference and experiment data for immunologists. ImmPort provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data.
Allele Frequency Net Database (AFND)The Allele Frequency Net Database (AFND) provides a central source, freely available to all, for the storage of allele frequencies from different polymorphic areas in the Human Genome. Users can contribute the results of their work into one common database and can perform database searches on information already available.
FungalRVAdhesin Prediction and Immunoinformatics portal for human fungal pathogens.
MAPPPMAPPP will predict possible antigenic peptides to be processed and finally presented on cell surfaces. This database aides in the prediction of immunodominant T-cell epitopes and is able to predict the proteasomal cleavage of proteins into smaller fragments, and the binding of peptide sequences to MHC class I molecules.
ProtScaleComputes and represents the profile produced by any amino acid scale on a selected protein.
ABCPredThis tool is an artificial neural network based B-cell epitope prediction server.
MIF AntigenicityThis tool predicts antigenic sites in proteins.
BcePredThis tool predicts continuous B-cell epitopes in antigenic sequences using physico-chemical properties.
SUPERFICIALIdentification of potential epitopes or binding sites.

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Antibody Related Links
TitleDescription
IMGTIMGT®, the international ImMunoGeneTics information system® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) and MhcSF, created in 1989 by Marie-Paule Lefranc (Université Montpellier II, CNRS). IMGT® consists of sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMER-DB), genome database (IMGT/GENE-DB) and structure database (IMGT/3Dstructure-DB), Web resources (IMGT Repertoire) and interactive tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/StructuralQuery, etc).
AAAAA(AHo's Amazing Atlas of Antibody Anatomy) The AAAAA aims to become the ultimate tool for antibody structural analysis, modeling and engineering.
ABG Antibody GroupThe ABG aims to investigate the relationships between the amino acid sequence, three-dimensional structure and the corresponding function of the antibody molecules, as a model of molecular recognition.
V BASE (the database of human antibody genes)V BASE is a comprehensive directory of all human germline variable region sequences compiled from over a thousand published sequences, including those in the current releases of the Genbank and EMBL data libraries. The database was developed at the MRC Centre for Protein Engineering.
NACCESSNACCESS is a stand-alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessibilities for both proteins and nucleic acids, and is available free for researchers at academic and non profit-making institutions.
GCG Wisconsin PackageFormally known as the GCG Wisconsin Package, DS GCG contains over 140 programs and utilities covering cross-disciplinary needs. DS GCG can be used to perform high-throughput or individual gene and protein analysis, and enables scientists within an organization to share their results and annotations.
The Antibody Resource Page Guide to antibody research and suppliers.
Mike's Ig Home Page Reference webpages on immunoglobulin structure and function prepared by Mike Clark, PhD, Cambridge University, Cambridge UK
WAMpredict Web Antibody ModelingThis tool predicts the WAM canonical classes and H3 C-terminal conformation (kinked or non-kinked) of a sequence, with which model quality can be assessed. In addition, WAMpredict will suggest a screen to select the conformation of the final model.
Therapeutic Antibody Center The TAC was originally set up in Cambridge by Geoff Hale and Herman Waldmann and operated there from 1990 to 1995. In collaboration with commercial sponsors, TAC has continued production of antibodies for non-commercial clinical trials and engaged in many other projects.
MSRS Catalog of primary antibodies MSRS offers an interactive searchable database containing a listing of 225,000 antibodies including some primary antibodies.
Antibody Structure and Sequence InformationThe Bioinformatics web site of Andrew C.R. Martin's Bioinformatics Group at UCL.

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Bioinformatics Resource Centers
TitleDescription
EuPathDBA portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Cryptosporidium, Encephalitozoon, Entamoeba, Enterocytozoon, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma).
ViPRA resource of genomic and research data and analysis tools for a wide range of human virus pathogens.
IRDA resource for the influenza virus research community that will facilitate an understanding of the influenza virus and how it interacts with the host organism, leading to new treatments and preventive actions.
PATRICPATRIC provides data and analysis tools for all bacterial species in the selected NIAID category A-C priority pathogens list.
PathogenPortalPathogen Portal is a repository linking to the Bioinformatics Resource Centers.
VectorBaseVectorBase is an NIAID Bioinformatics Resource Center dedicated to providing data to the scientific community for Invertebrate Vectors of Human Pathogens.

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MHC and TCR Related Links
TitleDescription
ASHI (American Society for Histocompatibility & Immunogenetics) ASHI is a not-for-profit association of clinical and research professionals including immunologists, geneticists, molecular biologists, transplant physicians and surgeons, pathologists and technologists. The society is dedicated to advancing the science and practice of immunogenetics and its impact on the quality of human life.
dbMHCThe dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human major histocompatibility complex (MHC). The MHC database currently consists of an interactive Alignment Viewer for HLA and related genes, an MHC microsatellite database, a sequence interpretation site for Sequencing Based Typing (SBT), and a Primer/Probe database. All reagents are characterized for allele specificity using the current curated WHO HLA allele database in cooperation with IMGT/HLA.
IMGTIMGT®, the international ImMunoGeneTics information system® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) and MhcSF, created in 1989 by Marie-Paule Lefranc (Université Montpellier II, CNRS). IMGT® consists of sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMER-DB), genome database (IMGT/GENE-DB) and structure database (IMGT/3Dstructure-DB), Web resources (IMGT Repertoire) and interactive tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/StructuralQuery, etc).

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Protein Related Links
TitleDescription
SwissProtThe UniProtKB/Swiss-Prot Protein Knowledgebase is a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and a high level of integration with other databases.
PDB (The Protein Data Bank) The single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
ExPASy (Expert Protein Analysis System) The ExPASy proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
GenBankGenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
TIGR (The Institute for Genomic Research) TIGR is a not-for-profit research institute whose primary research interests are in structural, functional and comparative analysis of genomes and gene products from a wide variety of organisms including viruses, Eubacteria, Archaea, and Eukaryotes.
PROWLPROWL provides an interactive environment for protein analysis easily accessed with any web browser over the internet. PROWL consists of a set of interconnected databases and software tools that enable swift analysis of protein mass spectrometry experiments.

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Laboratory Resources
TitleDescription
Biodefense and Emerging Infections Research Resources Repository (BEI Resources)BEI Resources was established by NIAID to acquire, authenticate, and produce reagents that scientists need to carry out basic research and develop improved diagnostic tests, vaccines, and therapies related to Category A, B, and C priority pathogens and emerging infectious disease agents.
NIAID Taconic Exchange Program/Taconic's Emerging Models ProgramTo foster increased availability to the scientific community of immunologically-related, gene-targeted mouse strains, the NIAID supports the NIAID Exchange Program with Taconic Farms, Inc, as part of their Emerging Models Program. The costs of the Exchange are partially underwritten by NIAID funds to provide the research community with ready access to emerging mouse models. Twenty-one mouse strains currently are available through the Exchange.
International Mouse Strain Resource (IMSR)The IMSR is a searchable online database of mouse strains and stocks available worldwide, including inbred, mutant, and genetically engineered mice. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research.
ATCC (American Type Culture Collection) ATCC is a global nonprofit biological resource center that provides biological products, technical services, and educational programs to private industry, government, and academic organizations around the world.
NIH-NIAID Tetramer Facility This facility provides custom synthesis and distribution of soluble MHC-peptide tetramer reagents that for use in staining antigen-specific T cells.

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Biodefense Resources
TitleDescription
NIAID Biodefense ResearchThis site contains biodefense-related information for biomedical researchers, the public, and the media.

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