TopMatch

TopMatch computes and ranks structural alignments and superpositions of protein structures to identify structural similarities and infer functional and evolutionary relationships between proteins.

Key Features:

• Structure alignment and superposition: Computes structural alignments and performs superposition of protein structures to compare 3D conformations.
• Multiple alignment generation: Computes and ranks multiple alternative alignments for a given pair of protein structures.
• Ranking by structural similarity: Ranks alignments based on measures of structural similarity.
• Alignment scoring: Calculates the degree of alignment between proteins.
• Identification of equivalent regions: Identifies and highlights structurally equivalent regions across compared proteins.
• 3D visualization of superpositions: Provides three-dimensional molecular visualization of superposed structures to inspect how specific regions align.

Scientific Applications:

• Comparative modeling: Reveals conserved structural cores and templates for homology- or comparative-model building.
• Protein engineering: Informs engineering decisions by identifying structurally equivalent residues and conformations.
• Phylogenetic analysis: Elucidates structural relationships that can reflect evolutionary links between protein families and classifications.

Methodology:

Computes structural alignments and superpositions, calculates degrees of alignment, and ranks multiple alignments by structural similarity.