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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
Presently, I am working as professor & head of Computational Biology, IIIT-Delhi. Before joining IIT Delhi, I worked as Scientist at Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh, India. More information is available from following sites Home Page of Gajendra P. S. Raghava's Group (http://www.imtech.res.in/raghava/) , Computational Resources for Drug Discovery (http://crdd.osdd.net/) , A Customized Operating System for Drug Discovery (http://osddlinux.osdd.net/)and and Gajendra Pal Singh Raghava - Wikipedia (https://en.wikipedia.org/wiki/Gajendra_Pal_Singh_Raghava) .
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.