MolLoc

MolLoc performs local, surface-oriented structural comparisons of molecular surfaces using protein structures in PDB format to identify and quantify similarities between binding sites, cavities, or selected residues for applications such as drug design and large-scale structural analyses.

Key Features:

• Input format: accepts protein structures in PDB format for surface comparison.
• Target regions: compares binding sites, cavities, or selected residues between structures.
• Comparison modes: supports pairwise comparisons and query-versus-list comparisons for large-scale structural analyses.
• Surface-oriented local comparison: focuses on local surface similarities independent of global sequence or fold similarity.
• Alignment strategy: generates structural alignments that maximize surface superimposition between compared molecules.
• Physicochemical matching: identifies pairs of atoms with similar physicochemical properties that are spatially proximate after superimposition.
• Optimization: derives an optimized rototranslation from matched atom pairs to achieve the best surface superimposition based on shared physicochemical characteristics.

Scientific Applications:

• Local surface similarity detection: detecting local surface similarities between molecules with different sequences and folds.
• Drug design and structural compatibility analysis: assessing structural compatibilities for ligand binding and molecular recognition in drug design.
• Large-scale structural analyses: comparing a query structure against a list of structures to identify similar molecular surfaces at scale.

Methodology:

Generates a structural alignment that maximizes surface superimposition; identifies pairs of atoms with similar physicochemical properties that are spatially proximate after superimposition; derives an optimized rototranslation from these atom pairs to achieve the best superimposition based on shared physicochemical characteristics.