LS-SNP

LS-SNP annotates human non-synonymous single nucleotide polymorphisms (nsSNPs) by mapping them onto Protein Data Bank (PDB) three-dimensional structures to provide structural annotations and visualizations for assessing potential functional impacts.

Key Features:

• Automated high-throughput pipeline: Maps human nsSNPs onto PDB structures and systematically updates the database via an automated build process.
• Biologically relevant structural annotations: Annotates features inferred from experimental three-dimensional protein structures to characterize potential effects of amino acid changes.
• UCSF Chimera molecular graphics: Produces high-quality three-dimensional renderings of nsSNPs on PDB structures using UCSF Chimera.

Scientific Applications:

• Identification of function-altering variants: Enables identification of nsSNPs that are likely to affect protein function by placing variants in structural context.
• Assessment of structural consequences: Supports analysis of potential impacts on protein stability, interactions, and activity by mapping amino acid changes onto structures.
• Pharmacogenomics and drug research: Informs studies in pharmacogenomics, drug development, and personalized medicine by linking genetic variation to structural effects.

Methodology:

The automated pipeline extracts relevant genomic data, aligns sequences to PDB protein structures, maps nsSNP positions onto those structures, annotates structural features inferred from experimental 3D data, and uses UCSF Chimera for molecular rendering.