LAHMA

LAHMA annotates and compares protein structure models by matching homologous amino acids to analyze structural features and assess model quality against homologs in the PDB-REDO database.

Key Features:

• Comprehensive homolog comparison: Compares a protein structure model against its close homologs in the PDB-REDO database to provide exhaustive homolog-based context.
• Sequence space visualization: Visualizes structural features in sequence space to identify differences between homologous structure models.
• Structural feature annotation: Annotates structural features at the amino-acid level to highlight variations that may affect function or stability.
• Structure-quality plots (e.g., Ramachandran plot): Generates and compares structure-quality plots such as Ramachandran plots to assess conformational quality of models.

Scientific Applications:

• Structural analysis: Facilitates comparative analysis of homologous protein models to investigate evolutionary relationships and structural variation.
• Model validation: Supports validation of predicted or experimentally determined structures by comparison with homologous entries from PDB-REDO.
• Functional annotation: Aids annotation of structural features that may correlate with specific biological functions or molecular interactions.

Methodology:

Compares structure models using data from the PDB-REDO database and integrates sequence-space visualization with structural feature annotation.