LGA

LGA performs structural alignment of protein structures and fragments, enabling sequence-dependent and sequence-independent comparisons to quantify three-dimensional similarity.

Key Features:

• Dual Comparison Modes: Supports sequence-dependent and sequence-independent structural comparisons.
• Scoring Function Integration: Generates alignment data that can be used in scoring functions to rank similarity between two protein structures.
• Structure Classification: Capable of classifying protein structures from comparative alignments.
• Clustering Capability: Enables clustering of similar fragments of protein structures.

Scientific Applications:

• Evolutionary analysis: Facilitates inference of evolutionary relationships through comparative structural similarity.
• Functional similarity assessment: Aids identification of functional similarity by comparing three-dimensional structures.
• Interaction inference: Assists in proposing potential protein–protein or protein–ligand interactions based on structural correspondence.
• Protein family and domain analysis: Supports classification and clustering of families and domains from structural fragments.

Methodology:

LGA applies a local-global alignment approach and provides both sequence-dependent and sequence-independent comparison modes for structural alignment.