VASE

VASE visualizes HSSP multiple sequence alignments and entropy/variability data on Protein Data Bank (PDB) 3D protein structures to support analysis of conserved and variable sites.

Key Features:

• Protein structure retrieval: Accepts Protein Data Bank (PDB) identifiers to retrieve 3D structures and associate structural coordinates with alignment positions.
• HSSP multiple sequence alignments: Uses HSSP (Homology-derived Secondary Structure of Proteins) multiple sequence alignments linked to target structures.
• Entropy/variability metrics: Presents entropy and variability information for aligned sequences to indicate sequence conservation and diversity across homologs.
• Secondary-structure and conservation mapping: Maps secondary-structure elements and conserved regions onto 3D models to correlate structural context with alignment-derived signals.

Scientific Applications:

• Comparative and evolutionary analysis: Enables comparative analyses of protein families to interpret conserved and variable sites in an evolutionary context.
• Functional and stability inference: Supports interpretation of the functional implications of conserved residues and variable sites for protein stability and function.
• Structural genomics: Facilitates structural genomics studies by linking sequence conservation patterns to solved PDB structures.
• Structure-guided drug design: Provides structural context for conserved and variable regions to inform drug design.

Methodology:

VASE retrieves HSSP alignments and structural information from the Protein Data Bank (PDB) and processes these data to generate visual representations that highlight secondary structures, conserved regions, and entropy/variability across homologous sequences.