3DBIONOTES

3DBIONOTES integrates and visualizes protein structure, sequence, and biological annotations to assess consistency between macromolecular structural models and biological data.

Key Features:

• Integration of Structural Data: Annotation of biochemical and biomedical information onto macromolecular structural models, complementing Protein Data Bank (PDB) entries with annotations from Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta, and dSysMap.
• Genomic Variant Analysis: Contingency analysis of genomic variants and amino acid features using Fisher exact tests, with integration of gene annotation viewers and protein-protein interaction visualization at the network level.
• COVID-19 Specific Tools: 3DBionotes-COVID-19 enables exploration of multiomics data and structural information and incorporates advanced validation metrics for cryo-electron microscopy (cryo-EM) studies.

Scientific Applications:

• Disease Research: Linking genomic variants to protein structures and functions to elucidate molecular mechanisms of diseases associated with single nucleotide polymorphisms affecting critical protein regions.
• Structural Biology: Validation and interpretation of structural models obtained by cryo-electron microscopy (cryo-EM), X-ray crystallography, and NMR spectroscopy.
• Viral Research: Integration of new viral structural data with genomics and interactomics to study viral proteins using the 3DBionotes-COVID-19 module.

Methodology:

3DBionotes employs a web-based framework that integrates multiple web services and interactive viewers.