MutDB

MutDB annotates non-synonymous single nucleotide polymorphisms (SNPs) and amino acid substitutions with protein structural information to assess their potential impact on human phenotypes and diseases.

Key Features:

• Integration with Structural Data: Annotates SNPs and amino acid substitutions with available protein structural information to map substitutions onto three-dimensional structures.
• Database Integration: Integrates variant and protein records from dbSNP and Swiss-Prot and incorporates disease-associated mutations and SNPs from the UCSC Annotated Genome and the human RefSeq gene set (~8,000 entries).
• Visualization Plugins: Provides plugins compatible with UCSF Chimera and PyMOL to visualize and model amino acid substitutions on protein structures.
• Web Services Interface: Exposes a web services interface for programmatic access to annotations and datasets.
• Functional Impact Prediction: Includes comparative genomic data and multiple sequence alignment–based conservation analyses with mutation maps at gene and protein levels to rank predicted functional consequences.

Scientific Applications:

• Disease Variant Interpretation: Assessing the molecular basis of diseases by providing structural context and predicted functional impacts of SNPs and mutations.
• Variant Prioritization: Identifying polymorphisms likely to alter protein function through conservation-based ranking using multiple sequence alignments.
• Genotype–Phenotype Analysis: Supporting studies of genotype-phenotype relationships and prioritization of variants for downstream therapeutic investigation.

Methodology:

Genetic variations from dbSNP, Swiss-Prot, the UCSC Annotated Genome, and RefSeq were annotated with protein structural data and conservation from multiple sequence alignments and integrated into visualization plugins and web services.