Offers methods for structure prediction, design, and remodeling of proteins and nucleic acids. Rosetta provides a comprehensive software suite for modeling macromolecular structures. This resource permits users to: (i) understand macromolecular interactions, (ii) design custom molecules, (iii) develop ways to search conformation and sequence space, and (iv) find energy functions for various biomolecular representations.
Models tumor immune evasion by integrating expression signatures of T cell dysfunction and T cell exclusion. TIDE identifies factors that determine these two mechanisms of tumor immune escape. This tool integrates data from 189 human cancer studies including up to 33 000 samples. The generated signatures enable immune checkpoint blockade (ICB) clinical response based on pre-treatment tumor profiles.
Assists users in detecting antigenic variance. CE-BLAST is an online tool that identifies the potential cross-reactive epitope between the recent zika pathogen and the dengue virus. It enables the design of cross-protective vaccines against emerging pathogens. Moreover, it aims to compare the conformational epitopes directly to suggest the relative antigenicity distance between antigens.
Offers a method for measuring variant surface glycoprotein (VSG) diversity across strains and during infections. VAPPER supplies a method allowing users to study the host–parasite interaction at population and individual scales. It can be used for analyzing antigenic diversity in systems data (genomes, transcriptomes, and proteomes) called variant antigen profiling (VAP).
A laboratory software solution for research in the digital age. AirLab facilitates organization of data on large collections of antibody stocks and streamlines the processes of purchasing, storage, antibody panel creation, results logging, and antibody validation data sharing and distribution. Designed with antibody-based experiments in mind, the software can be easily adapted to tracking of any type of reagent and any type of high- or low-throughput experiment. The cloud-based platform in conjunction with mobile gadgets enables ready access to relevant information, reducing the logistical overhead of research that has become increasingly convoluted due to application of multiparametric experiments.
Provides a means to model T cell receptors (TCRs) structures from sequence. TCRmodel is a TCR modeling server that provides three options to generate TCR structural models from sequence: (i) users can enter amino acid sequences containing TCR and variable domains (ii) user can specify TCR TRAV/TRAJ and TRBV/TRBJ germline genes and CDR3 amino acid sequences, and (iii) users can submit files containing sequences of one or more TCRs in FASTA format for batch processing.
Aims to manipulate, analyze and visualize antibody repertoire sequence data. BRepertoire is a web application that can be used for T cell and non-human sequencing data. This tool supports the calculation of a set of statistical significance and effect size measures. The calculation and analysis of physico-chemical properties provides a representation of amino acid sequences.
Aims to enhance the interpretation of murine gene expression data for human immune disease studies. mEBT is a web server that uses a given expression data of murine experiments in a two-class condition for (i) finding multiple matching experiment profiles from the database, (ii) calculating pseudo variances, and (iii) providing significant genes that are likely to have similar responses in the corresponding human condition.
Assembles and serves for visualization of known immune response to a specific antigen. ImmunomeBrowser aggregates all data relevant to the user query on the web application and illustrates knowledge gaps in a reference protein. This tool only supports data derived from Immune Epitope Database (IEDB) queries and not with user datasets. It can also be utilized to analyze immunogenicity testing of therapeutic protein.
Detects characteristics related with viral antigenicity. GG-MTSL consists of model able to be trained from multi-sourced serologic data with the aim of recognizing variants and describing antigenic profiles in real time and on a large scale. This program provides a quantitative feature that starts from hemagglutinin (HA) protein sequences to evaluate antigenic distances between influenza A viruses.
Enables analysis of multicell-per-well sequencing data. MAD-HYPE consists of a Bayesian approach that identifies T cell receptor (TCR) αβ pairings using subsampled T cell populations. The software resolves paired-chain sequencing data from multicell-per-well sequencing experiments and can enhance the identification rates for high-throughput antigen receptor pairing. It was validated in the context of simulated datasets drawn from observed parameters, as well as on experimental samples.
Detects antigen epitopes. Glep is an antibody-agnostic epitope prediction algorithm that detects single, multi-separated, as well as overlapping epitopes from antigens, assuming the data of the corresponding antibodies are not given. The software is composed of three steps: (1) construction of a residue-level graph of an antigen, (2) partition of the graph into subgraphs, and (3) classification of each expanded subgraph as an epitope or a non-epitope by support vector machine (SVM).
Predicts and analyzes combination antibody neutralization scores using IC50 and/or IC80 for individual antibodies. CombiNaber is a web-tool that predict bnAb combination neutralization results from single bnAb neutralization data using either “Bliss-Hill” (BH) or additive models and perform systematic analysis. It provides the user with the best candidate combinations for their panel. The predicted scores are systematically compared for all single antibodies and 2, 3 and 4 antibody combinations analyzed.
Estimates the relative immune cell response for each cell type. ICEPOP uses gene names and the associated expression values from microarray data of mouse and human organ or tissue samples to work. It calculates the relative response scores for each immune cell type defined by the reference matrix made from public gene expression databases. It can analyze non-purified bulky samples such as whole organs or biopsy tissue.
Constructs antibody models by simulating the natural evolution of antibody generation and affinity maturation. OptMAVEn can reduce the potent immunogenicity of designed antibody models and optimize their binding affinity to an antigen. It enables to (1) locate antigens in the antibody-binding site, (2) rediscover native antibody parts, (3) recapitulate known interactions responsible for affinity maturation and (4) unambiguously distinguish human antibody sequences from other species.
Automates the gene feature annotation information and deviations of novel allele from the identified closest known allele requiring minimal intervention. TypeLoader facilitates submission of full-length genomic allele sequences. It aims to aid in the curation and submission of new full-length human leukocyte antigen (HLA) alleles. This tool allows to submit immunogenetics sequence repositories whilst minimizing errors that easily occur otherwise.
Determines the p-values associated with peptide enrichments. PhIP-seq Analyzer is based on a generalized Poisson (GP) model. It can launch the sequencing alignments, reads counting, data normalization and z-score statistics, sequencing quality control, polynomial regression or enrichment investigation. This tool can serve to retrieve and interpret antibody binding specificities.
Calculates the probability of generating a given CDR3 amino acid sequence or motif. OLGA implements an exact computation of the generation probability of any B-cell receptor (BCR) or T-cell receptor (TCR) sequence or motif. The software can compute the probabilities of CDR3 sequences and motifs, with or without V/J restriction, of 4 chain loci, but the list can be expanded. It can serve to compute baseline receptor frequencies and to identify outlying sequences in repertoire sequencing datasets.
Enables users to predict of epitope-specific T-cell receptor (TCR) sequences. TCRex can be used for the identification of T-cell receptor repertoire targets. Predictions can be made for various cancer and viral epitopes present in the included database or for new epitopes by training new prediction models. This tool is based on the principle that similar TCR sequences often target the same epitope and that machine learning techniques can be used to learn those commonalities shared by epitope-specific TCR sequences.
Identifies evolving immunoglobulin G (IgC) responses for up to 500 known human viruses when applied to VirScan analysis of longitudinally collected serum samples. AVARDA measures confidence of infection via VirScan peptide enrichment Z-scores. This tool furnishes a probabilistic assessment of infection by examining alignment of all library peptides to each other and to all human viruses.
Detects perturbed molecular processes in complex human diseases. MultiPLIER offers an unsupervised transfer learning framework with a focus on investigating rare diseases. This program assists users in interpreting disease expression data from multiple tissues. It aims to provide a transfer learning strategy dedicated to the analysis of systems and discovery-driven research dealing with mechanisms linked to human diseases.
Allows users to perform antibody library screening. TrueRepertoire is a high-throughput cloning platform based on a combination of micro biochip and laser-based isolation. This program intends to perform in-depth analysis of phage display library as well as retrieval of the clones’ physical DNA, including rare ones. Additionally, it enables the conservation of linkage information between both heavy and light chains of the clones.
Performs an unsupervised data structure deconvolution and mapping to external knowledge. PLIER intends to minimize noise and identify regulation in cell-type proportions or pathways. This software proceeds by approximating the expression pattern of every gene as a linear combination of eigengene-like latent variables (LVs). It can maximize statistical power and detect specific upstream pathways or cell type proportion by integrating dataset deconvolution with prior knowledge.
Permits users to visualize antibody lineage tree structure. COLT-Viz allows interactive exploration of lineage trees with multiple antibody sequence properties encoded and automatically checked when the tree structure is manually altered. It is able to find interesting patterns of antibody evolution process and select interesting nodes for further evaluation. This tool can check isotype constraint and time constraint.
Enables peptide design. OptimumAntigen™ Design Tool allows: avoidance of unexposed epitopes, ability to specify desired cross-reactivity, antigenicity of chosen peptide, identification of the best conjugation and presentation options for users desired assay(s), use of built in peptide tutorial for synthesis and solubility, as well as guaranteed immune response.
Allows users to rank seroreactivity profiles using an assortement of supervised statistical learning approaches. SePaCS is a web application that can be performed from several human diseases such as autoimmune diseases and tumor entities. It contains approaches including support vector machines, linear and diagonal discriminant analysis. The application can be run by using both a training and a test set as antibody profile sets or only with a test set.
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