TANTIGEN is an online database of T-cell epitopes and HLA ligands . A new version of TANTIGEN is introduced this month, known as TANTIGEN 2.0. In this article, we give a brief introduction to this new version of the database.
TANTIGEN is a comprehensive database consisting of 1000 T cell epitopes and HLA ligands from 292 different tumor T-cell antigens . The latest version, TANTIGEN 2.0 consists of 4,296 antigen variants from 403 unique tumor antigens and more than 1500 T-cell epitopes and HLA ligands . It also contains TCR sequences extracted from Human Pathology Atlas. The new data is incorporated from the Cancer Antigenic Peptide Database  and recent publications.
Different bioinformatics tools are incorporated in the TANTIGEN 2.0 for data analysis including BLAST and MAFFT for similarity search and multiple sequence alignment. It also consists of a set of visualization tools that highlight the peptides located within their parent proteins .
TANTIGEN 2.0 webserver is constructed in KB-builder framework and is freely accessible at http://projects.met-hilab.org/tadb.
For more information, click here.
- Olsen, L. R., Tongchusak, S., Lin, H., Reinherz, E. L., Brusic, V., & Zhang, G. L. (2017). TANTIGEN: a comprehensive database of tumor T cell antigens. Cancer Immunology, Immunotherapy, 66(6), 731-735.
- Zhang, G., Chitkushev, L., Olsen, L.R. et al. (2021). TANTIGEN 2.0: a knowledge base of tumor T cell antigens and epitopes. BMC Bioinformatics 22, 40.
- Vigneron, N., Stroobant, V., Van den Eynde, B. J., & van der Bruggen, P. (2013). Database of T cell-defined human tumor antigens: the 2013 update. Cancer Immunity Archive, 13(3).
cheML.io: ML-generated molecules database
Due to the advancement of machine learning (ML) methods, we can find increasing applications of them in the field of bioinformatics as well. ML is being utilized in making personalized medicines, similarity searches in DNA and protein sequences, phylogenetics by mapping selected species on phylogenetic trees, gene and protein function annotation, generating chemical compounds, and so on. In this article, we will discuss an online database of ML-generated molecules known as cheML.io .
MitoTox- A new mitochondrial toxicity database
H2V- A Database of Human Responsive Genes & Proteins for SARS & MERS
How to download small molecules from ZINC database for virtual screening?
It is difficult to manage thousands of compounds altogether while performing virtual high-throughput screening. Compounds databases allow to download of molecules in different formats such as the ZINC database  allows downloading a batch file that is processed afterward. In this article, we will download small molecules from the ZINC database  that can be used in virtual screening. (more…)