Aquaria

Aquaria maps protein sequences to 3D structures and integrates sequence annotations and variation onto structural coordinates to support interpretation of protein structure–function relationships.

Key Features:

• Sequence-centric mapping: Uses protein sequence as the primary entry point to retrieve and organize all structure models linked to that sequence.
• Precalculated comparisons: Precalculates an all-against-all comparison between Swiss-Prot and PDB sequences, updated monthly.
• Grouping and ranking: Groups structures by sequence alignment and oligomeric state and ranks them by similarity to the target sequence.
• Large-scale alignments: Includes tens of millions of precalculated sequence-to-structure alignments and structural coverage for most Swiss-Prot proteins.
• Residue-level mapping: Maps sequence-level variation (identical, conserved, and non-conserved residues) with graded coloring directly onto 3D coordinates.
• Annotation overlays: Overlays sequence feature annotations from UniProt and InterPro, including domains, variants, SNPs, and post-translational modifications.

Scientific Applications:

• Variant and PTM interpretation: Interprets sequence variants and post-translational modifications in their 3D structural context using UniProt and InterPro annotations.
• Comparative structural analysis: Compares structural homologs and oligomeric states via Swiss-Prot–PDB sequence comparisons and alignment-based ranking.
• Coverage assessment: Assesses structural coverage across Swiss-Prot at scale using the precalculated sequence-to-structure alignments.

Methodology:

Precalculates all-against-all comparisons between Swiss-Prot and PDB sequences (updated monthly), groups structures by sequence alignment and oligomeric state, ranks structures by sequence similarity to the target, maps residue conservation status (identical, conserved, non-conserved) onto 3D coordinates, and overlays UniProt and InterPro feature annotations.