QSalignWeb

QSalignWeb predicts and analyzes protein quaternary structures to infer their physiological relevance by identifying structural conservation among homologs, including user-submitted homo-oligomeric structures.

Key Features:

• User-submitted and non-PDB structures: Accepts user-uploaded homo-oligomeric protein structures rather than restricting analysis to Protein Data Bank (PDB) entries.
• Sequence and PFAM domain analysis: Extracts sequence from the submitted structure and searches for homologous proteins using sequence similarity and PFAM domain architecture.
• Physiological relevance inference: Infers physiological relevance by detecting structural conservation between the query quaternary structure and homologous structures.
• PISA-based alternative QS generation: Uses PISA to generate alternative quaternary structures from the submitted structure and processes these alternatives equivalently to the original query.
• Representative family quaternary structures: Reports representative QSs within the protein family to suggest possible quaternary arrangements and provide starting points for homology modeling.

Scientific Applications:

• Analysis of novel or underrepresented proteins: Enables quaternary-structure analysis for proteins that lack or have limited representation in the PDB by accepting user-submitted structures.
• Assessment of physiological relevance: Provides evidence for or against the physiological relevance of observed crystal assemblies via structural conservation among homologs.
• Homology modeling of quaternary arrangements: Supplies representative family QSs that can serve as starting models for quaternary-level homology modeling.
• Hypothesis generation and experimental design: Generates alternative QSs and conserved-family examples to inform testable hypotheses about oligomeric state and interface architecture.

Methodology:

Extracts sequence from the submitted structure; performs sequence-based searches for homologous structures using sequence similarity and PFAM domain architecture; detects structural conservation between the query quaternary structure and homologs to infer physiological relevance; uses PISA to generate alternative quaternary structures from the submitted structure and processes these alternatives equivalently.