3DVizSNP

3DVizSNP visualizes missense mutations on protein structures to provide structural context for assessing variant impacts.

Key Features:

• Integration with iCn3D: Uses the iCn3D platform to render and explore three-dimensional protein structures and annotations.
• Python-Based Implementation: Implemented in Python for local execution and programmatic use.
• REST API Utilization: Employs REST APIs to streamline data processing and visualization tasks.
• Variant File Processing: Processes variant caller format files containing identified missense mutations.
• Structure Selection: Automatically selects structural models from the Protein Data Bank (PDB) or AlphaFold when mapping mutations.
• Structural Contact Analysis: Leverages iCn3D annotations and analysis capabilities to assess changes in structural contacts caused by mutations.

Scientific Applications:

• Mutation Impact Assessment: Prioritizes missense variants based on their potential effects on protein structure and function.
• Cancer Genomics: Screens large sets of cancer-associated sequence variants for structural implications to identify potential oncogenic mutations.
• Drug Target Identification: Visualizes mutation-induced alterations in protein structures to inform drug binding site analysis and therapeutic target selection.

Methodology:

Processes variant caller format files to map missense mutations onto protein structures, automatically selects models from PDB or AlphaFold, and uses iCn3D annotations and REST APIs within a Python implementation to visualize and analyze structural contacts.