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Critical role of glycosylation in determining the length and structure of T cell epitopes - As suggested by a combined in silico systems biology approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions The findings of this bioinformatical approach shed light on fundamental factors that might have shaped adaptive immunity during evolution. Our data suggest that amino acid sequence-based hypo/non-glycosylation of certain segments of proteins might be substantial for determining T cell immunity/autoimmunity. (Source: Immunome Research)
Source: Immunome Research - September 23, 2009 Category: Allergy & Immunology Authors: Tamas SzaboRobin PalotaiPeter AntalItay TokatlyLaszlo TothfalusiOle LundGyorgy NagyAndras FalusEdit Buzas Source Type: journals

Of mice and humans: how good are HLA transgenic mice as a model of human immune responses?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These data suggest that differences in immunodominance patterns might explain the incomplete response overlap, and that with limitations, HLA Tg mice represent a relevant and suitable model system to study immune responses against complex pathogens. (Source: Immunome Research)
Source: Immunome Research - June 16, 2009 Category: Allergy & Immunology Authors: Maya KotturiErika AssarssonBjoern PetersHoward GreyCarla OseroffValerie PasquettoAlessandro Sette Source Type: journals

Functional recombinant MHC class II molecules and high-throughput peptide-binding assaysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have successfully developed versatile MHC-II resources, which may assist in the generation of MHC class II -wide reagents, data, and tools. (Source: Immunome Research)
Source: Immunome Research - May 5, 2009 Category: Allergy & Immunology Authors: Sune Justesen, Mikkel Harndahl, Kasper Lamberth, Lise-Lotte B Nielsen and Soren Buus: Source Type: journals

Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chainsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We hypothesize that peripheral autoreactivity results primarily from somatic mutation, and that the genetic correlates of autoreactivity in mature B-cells are not the same as those for autoreactivity in immature B cells. What is seen in mature autoreactive B cells are the correlates of {\it autoreactive potential}, not of autoreactivity per se. The autoreactive potential is higher for V(D)J rearrangements encoded to a large extent by N-nucleotides rather than by the gene segments that, we posit, have been selected in germline evolution for their suppression of autoreactive potential. (Source: Immunome Research)
Source: Immunome Research - February 27, 2009 Category: Allergy & Immunology Authors: Joseph M Volpe and Thomas B Kepler Source Type: journals

Data mining of cancer vaccine trials: a bird's-eye viewEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We have developed a data mining approach that enables rapid extraction of complex data from the major clinical trial repository. Summarization and visualization of these data represents a cost-effective means of making informed decisions about the future cancer vaccine clinical trials. (Source: Immunome Research)
Source: Immunome Research - December 12, 2008 Category: Allergy & Immunology Authors: Xiaohong Cao, Karen B Maloney and Vladimir Brusic Source Type: journals

Peptide length significantly influences in vitro affinity for MHC class II moleculesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The observed relationship between peptide length and MHC class II affinity is likely to have clear implications for vaccine design and the study of immunological disease. (Source: Immunome Research)
Source: Immunome Research - November 26, 2008 Category: Allergy & Immunology Authors: Cathal O'Brien, Darren R Flower and Conleth Feighery Source Type: journals

Expression Analysis of G Protein-Coupled Receptors in Mouse MacrophagesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The constitutive or regulated expression in macrophages of several GPCRs identified in this study has not previously been described. Future studies on such GPCRs and their agonists are likely to provide important insights into macrophage biology, as well as novel inflammatory pathways that could be future targets for drug discovery. (Source: Immunome Research)
Source: Immunome Research - April 29, 2008 Category: Allergy & Immunology Authors: Jane E Lattin, Kate Schroder, Andrew I Su, John R Walker, Jie Zhang, Tim Wiltshire, Kaoru Saijo, Christopher K Glass, David A Hume, Stuart Kellie and Matthew J Sweet Source Type: journals

Efficiency of the immunome protein interaction network increases during evolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results shed light on selective forces acting on the emergence of biological networks. It is likely that the high efficiency and low vulnerability are intrinsic properties of many biological networks, which arise from the effects of evolutionary processes yet to be uncovered. (Source: Immunome Research)
Source: Immunome Research - April 22, 2008 Category: Allergy & Immunology Authors: Csaba Ortutay and Mauno Vihinen Source Type: journals

Large-scale analysis of human heavy chain V(D)J recombination patternsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We present here the most precise estimates of gene segment usage frequencies currently available along with analyses regarding n-nucleotide distributions and D-J segment pair preferences. Additionally, we provide the first statistical evidence that sequential D-J recombinations occur at the human heavy chain locus during B-cell ontogeny with an approximate frequency of 20%. (Source: Immunome Research)
Source: Immunome Research - February 27, 2008 Category: Allergy & Immunology Authors: Joseph M Volpe and Thomas B Kepler Source Type: journals

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide librariesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These data confirm, on a large scale, including 15 human and 4 mouse class I alleles, the efficacy of the positional scanning combinatorial library approach for describing MHC class I binding specificity and identifying high affinity binding peptides. These libraries were shown to be useful for identifying specific primary and secondary anchor positions, and thereby simpler motifs, analogous to those described by other approaches. The present study also provides matrices useful for predicting high affinity binders for several alleles for which detailed quantitative descriptions of binding specificity were prev...
Source: Immunome Research - January 25, 2008 Category: Allergy & Immunology Authors: John Sidney, Erika Assarsson, Carrie Moore, Sandy Ngo, Clemencia Pinilla, Alessandro Sette and Bjoern Peters Source Type: journals

Analysis and prediction of protective continuous B-cell epitopes on pathogen proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Background: The application of peptide based diagnostics and therapeutics mimicking part of protein antigen is experiencing renewed interest. So far selection and design rationale for such peptides is usually driven by T-cell epitope prediction, available experimental and modelled 3D structure, B-cell epitope predictions such as hydrophilicity plots or experience. If no structure is available the rational selection of peptides for the production of functionally altering or neutralizing antibodies is practically impossible. Specifically if many alternative antigen are available the reduction of required synthesized peptides...
Source: Immunome Research - January 7, 2008 Category: Allergy & Immunology Authors: Johannes Sollner, Rainer Grohmann, Ronald Rapberger, Paul Perco, Arno Lukas and Bernd Mayer Source Type: journals

An analysis of the epitope knowledge related to MycobacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: All current TB-related epitope data was cataloged for the first time from the published literature. The resulting inventory of more than a thousand different epitopes should prove a useful tool for the broad scientific community. Knowledge gaps specific to TB epitope data were also identified. In summary, few non-peptidic or post-translationally modified epitopes have been defined. Most importantly epitopes have apparently been defined from only 7% of all ORFs, and the top 30 most frequently studied protein antigens contain 65% of the epitopes, leaving the majority of M. tuberculosis genome unexplored. A lack ...
Source: Immunome Research - December 14, 2007 Category: Allergy & Immunology Authors: Martin J Blythe, Qing Zhang, Kerrie Vaughan, Romulo de Castro, Nima Salimi, Huynh-Hoa Bui, David M Lewinsohn, Joel D Ernst, Bjoern Peters and Alessandro Sette Source Type: journals

Amino acid biophysical properties in the statistical prediction of peptide-MHC class I bindingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Representation of amino acids using a few important bio-physio-chemical property provide a natural basis for representing peptides and greatly improves peptide-MHC class I binding prediction. (Source: Immunome Research)
Source: Immunome Research - October 29, 2007 Category: Allergy & Immunology Authors: Surajit Ray and Thomas B Kepler Source Type: journals

Using the natural evolution of a rotavirus-specific human monoclonal antibody to predict the complex topography of a viral antigenic siteEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The use of mutagenesis constraints in docking calculations allows for the identification of a small number of alternative arrangements of the antigen-antibody interface. The mutagenesis information from the natural evolution of a neutralizing antibody can be used to discriminate between residue-scale models and create distance constraints for atomic-resolution docking. The integration of binding affinity data or other information with computation may be an advantageous approach to assist peptide engineering or therapeutic antibody design. (Source: Immunome Research)
Source: Immunome Research - September 18, 2007 Category: Allergy & Immunology Authors: Brett A McKinney, Nicole L Kallewaard, James E Crowe and Jens Meiler Source Type: journals

In silico characterization of immunogenic epitopes presented by HLA-Cw*0401Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The analysis of predicted Cw*0401-binding peptides showed that anchor residues may not be restrictive and the Cw*0401 binding pockets may possibly accommodate a wide variety of peptides with common physico-chemical properties. The potential Cw*0401-specific T-cell epitope repertoires for HIV-1 p24gag and gp160gag glycoproteins are well distributed throughout both glycoproteins, with thirteen and nine immunological hot spots for HIV-1 p24gag and gp160gag glycoproteins respectively. These findings provide new insights into HLA-C peptide selectivity, indicating that pre-selection of candidate HLA-C peptides may o...
Source: Immunome Research - August 20, 2007 Category: Allergy & Immunology Authors: Joo Chuan Tong, Zong Hong Zhang, J. THOMAS August, Vladimir Brusic, Tin Wee Tan and Shoba Ranganathan Source Type: journals

IDR knowledge base for primary immunodeficienciesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The IDR is the first knowledge base specifically designed to capture in a systematic and validated way both clinical and molecular information for primary immunodeficiency. The service is freely available at http://bioinf.uta.fi/idr and is regularly updated. The IDR facilitates primary immunodeficiency informatics and helps to parameterise in silico modelling of these diseases. The IDR is useful also as an advanced education tool for medical students, and physicians. (Source: Immunome Research)
Source: Immunome Research - March 29, 2007 Category: Allergy & Immunology Authors: Crina Samarghitean, Jouni Valiaho and Mauno Vihinen Source Type: journals

Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction toolsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A heuristic-based method of combining the results of the individual tools better facilitates the scanning of large proteomes for potential epitopes, yielding more actual high-affinity binders while reporting very few false positives. (Source: Immunome Research)
Source: Immunome Research - March 24, 2007 Category: Allergy & Immunology Authors: Brett Trost, Mik Bickis and Anthony Kusalik Source Type: journals

ImmTree: Database of evolutionary relationships of genes and proteins in the human immune systemEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: ImmTree provides a unique data set of genes and proteins from the human immune system, their phylogenetics, and information for comparisons of human-mouse ortholog pairs, synonymous and non-synonymous mutation rates, as well as other statistical information. (Source: Immunome Research)
Source: Immunome Research - March 21, 2007 Category: Allergy & Immunology Authors: Csaba Ortutay, Markku Siermala and Mauno Vihinen Source Type: journals

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required. (Source: Immunome Research)
Source: Immunome Research - February 21, 2007 Category: Allergy & Immunology Authors: John E Beaver, Philip E Bourne and Julia V Ponomarenko Source Type: journals

A novel strategy for the identification of antigens that are recognised by bovine MHC class I restricted cytotoxic T cells in a protozoan infection using reverse vaccinologyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The identification of an antigen containing multiple CTL epitopes and its apparent immunodominance during a protective anti-parasite response makes Tp2 an attractive candidate for evaluation of its vaccine potential. (Source: Immunome Research)
Source: Immunome Research - February 9, 2007 Category: Allergy & Immunology Authors: Simon P Graham, Yoshikazu Honda, Roger Pelle, Duncan M Mwangi, E Jane Glew, Etienne P de Villiers, Trushar Shah, Richard Bishop, Pierre van der Bruggen, Vishvanath Nene and Evans LN Taracha Source Type: journals

Protein sequence database for pathogenic arenavirusesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The database is available at http://epitope.liai.org:8080/projects/arena and can be used to aid in studies that require proteomic information from pathogenic arenaviruses. (Source: Immunome Research)
Source: Immunome Research - February 8, 2007 Category: Allergy & Immunology Authors: Huynh-Hoa Bui, Jason Botten, Nicolas Fusseder, Valerie Pasquetto, Bianca Mothe, Michael J. Buchmeier and Alessandro Sette Source Type: journals

In silicoidentification of opossum cytokine genes suggests the complexity of the marsupial immune system rivals that of eutherian mammalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The power of this approach was demonstrated by the identification of orthologous cytokines between marsupials and eutherians that share only 30% identity at the amino acid level. Furthermore, the presence of key immunological genes suggests that marsupials do indeed possess a sophisticated immune system, whose function may parallel that of eutherian mammals. (Source: Immunome Research)
Source: Immunome Research - November 10, 2006 Category: Allergy & Immunology Authors: Emily SW Wong, Lauren J Young, Anthony T Papenfuss and Katherine Belov Source Type: journals

PREDTAP: a system for prediction of peptide binding to the human transporter associated with antigen processingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: PREDTAP can be integrated with prediction systems for MHC class I binding peptides for improved performance of in silico prediction of T-cell epitopes. PREDTAP is available at http://antigen.i2r.a-star.edu.sg/predTAP. (Source: Immunome Research)
Source: Immunome Research - May 23, 2006 Category: Allergy & Immunology Authors: Guang L Zhang, Nikolai Petrovsky, Chee K Kwoh, J Thomas August and Vladimir Brusic Source Type: journals

Improved method for predicting linear B-cell epitopesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The best single method for predicting linear B-cell epitopes is the hidden Markov model. Combining the hidden Markov model with one of the best propensity scale methods, we obtained the BepiPred method. When tested on the validation data set this method performs significantly better than any of the other methods tested. The server and data sets are publicly available at www.cbs.dtu.dk/services/BepiPred. (Source: Immunome Research)
Source: Immunome Research - April 24, 2006 Category: Allergy & Immunology Authors: Jens Erik Pontoppidan Larsen, Ole Lund and Morten Nielsen Source Type: journals

Modeling the bound conformation of Pemphigus Vulgaris-associated peptides to MHC Class II DR and DQ AllelesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our docking simulations are entirely consistent with functional data obtained from in vitro competitive binding assays and T cell proliferation studies in DR4 and DR6 PV patients. Our findings ascertain that DRB1*0402 plays a crucial role in the selection of specific self-peptides in DR4 PV. DRB1*0402 and DQB1*0503 do not necessarily share the same core residues, indicating that both alleles may have different binding specificities. In addition, our results lend credence to the hypothesis that the alleles DQB1*0201 and *0202 play a protective role by binding Dsg3 peptides with greater affinity than the suscepti...
Source: Immunome Research - January 21, 2006 Category: Allergy & Immunology Authors: Joo Chuan Tong, Jeff Bramson, Darja Kanduc, Selwyn Chow, Animesh A Sinha and Shoba Ranganathan Source Type: journals

Prediction of MHC class II binding peptides based on an iterative learning modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The iterative learning procedure appears to be effective in prediction of MHC class II binders. It offers an alternative approach to this important predictionproblem. (Source: Immunome Research)
Source: Immunome Research - December 13, 2005 Category: Allergy & Immunology Authors: Naveen Murugan and Yang Dai Source Type: journals

Modelling vaccination schedules for a cancer immunoprevention vaccineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a systematic approach to search for an effective vaccination schedule using mathematical computerized models. Our study is based on our previous model that simulates the cancer vs immune system competition activated by tumor vaccine. This model accurately reproduces in-vivo experiments results on HER-2/neu mice treated with the immuno-prevention cancer vaccine (Triplex) for mammary carcinoma. In vivo experiments have shown the effectiveness of Triplex vaccine in protection of mice from mammary carcinoma. The full protection was conferred using chronic (prophylactic) vaccination protocol while therapeutic vaccina...
Source: Immunome Research - October 7, 2005 Category: Allergy & Immunology Authors: Santo Motta, Filippo Castiglione, Pierluigi Lollini and Francesco Pappalardo Source Type: journals

AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
AntiJen is a database system focused on the integration of kinetic, thermodynamic, functional, and cellular data within the context of immunology and vaccinology. Compared to its progenitor JenPep, the interface has been completely rewritten and redesigned and now offers a wider variety of search methods, including a nucleotide and a peptide BLAST search. In terms of data archived, AntiJen has a richer and more complete breadth, depth, and scope, and this has seen the database increase to over 31,000 entries. AntiJen provides the most complete and up-to-date dataset of its kind. While AntiJen v2.0 retains a focus on both T...
Source: Immunome Research - October 6, 2005 Category: Allergy & Immunology Authors: Christopher P Toseland, Debra J Clayton, Helen McSparron, Shelley L Hemsley, Martin J Blythe, Kelly Paine, Irini A Doytchinova, Pingping Guan, Channa K Hattotuwagama and Darren R Flower Source Type: journals

Immunome ResearchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Immunology research has been transformed in the post-genomics era, with high throughput molecular biology and information technologies taking an increasingly central role. This has led to the development of a new area of science termed "Immunomics", that encompasses genomic, high throughput and bioinformatic approaches to immunology. In recognition of the increasing importance of this field, Immunome Research is a new Open Access, online journal, that will publish cutting edge research across the field of Immunomics. Immunome Research will publish a wide range of article types including specialty immunology databases, immu...
Source: Immunome Research - September 20, 2005 Category: Allergy & Immunology Authors: Nikolai Petrovsky Source Type: journals

An ontology for immune epitopes: application to the design of a broad scope database of immune reactivitiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The IEDB's ontology is the first ontology specifically designed to capture both intrinsic chemical and biochemical information relating to immune epitopes with information relating to the interaction of these structures with molecules derived from the host immune system. We anticipate that the development of this type of ontology and associated databases will facilitate rigorous description of data related to immune epitopes, and might ultimately lead to completely new methods for describing and modeling immune responses. (Source: Immunome Research)
Source: Immunome Research - September 20, 2005 Category: Allergy & Immunology Authors: Muthuraman Sathiamurthy, Bjoern Peters, Huynh-Hoa Bui, John Sidney, John Mokili, Stephen S Wilson, Ward Fleri, Deborah L McGuinness, Philip E Bourne and Alessandro Sette Source Type: journals

IMGT, the international ImMunoGeneTics information system®: a standardized approach for immunogenetics and immunoinformaticsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
IMGT, the international ImMunoGeneTics information system®http://imgt.cines.fr, was created in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM) (Université Montpellier II and CNRS) at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) of any species which belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT consists of five databases, ten on-line tools and more than 8,000 ...
Source: Immunome Research - September 20, 2005 Category: Allergy & Immunology Authors: Marie-Paule Lefranc Source Type: journals