MSALigMap

MSALigMap maps active-site amino acid residues that interact with specific ligands from PDB structures onto target protein sequences using multiple sequence alignment to analyze binding-site conservation and predict mutation impacts.

Key Features:

• Ligand-Specific Mapping: Maps amino acid residues that bind selected ligands identified in PDB structures onto aligned target sequences.
• Novel Sequence Analysis: Accepts novel protein sequences not present in public databases for mapping against ligand-bound PDB structures.
• Comparative Analysis Across Sequences: Supports comparison of multiple protein sequences from different organisms or clinical strains against ligand- or drug-bound PDB structures.
• Mutation Impact Prediction: Facilitates prediction of functional consequences of mutations within mapped binding sites to assess effects on drug efficacy and resistance.

Scientific Applications:

• Drug Discovery and Development: Identifying critical ligand-binding residues to inform drug design and therapeutic target selection.
• Protein Engineering: Informing engineering of proteins with altered binding properties by revealing how mutations affect ligand interactions.
• Comparative Genomics: Mapping and comparing binding-site residues across species or strains for evolutionary and functional genomics studies.

Methodology:

MSALigMap uses multiple sequence alignment to align target protein sequences with sequences from PDB structures crystallized with specific ligands and maps the ligand-interacting residues from the PDB entries onto the aligned targets.