mTM-align

mTM-align performs fast database searches and accurate multiple protein structure alignments to compare protein structures from the Protein Data Bank (PDB).

Key Features:

• Fast Database Search: Implements a heuristic algorithm and a hierarchical organization of protein structures to accelerate database searches, typically taking 2–5 minutes for medium-sized proteins (~300 residues).
• Multiple Structure Alignment: Uses the mTM-align algorithm to perform multiple-structure alignments with improved speed and accuracy and can automatically align the top ten search hits or additional selected structures.
• Interplay Between Modules: Integrates the heuristic hierarchical search module with the mTM-align multiple-alignment module to enable rapid retrieval and precise alignment of related structures.

Scientific Applications:

• Comparative structural analysis: Rapidly compare and align multiple protein structures from the PDB for structural comparison studies.
• Evolutionary relationship inference: Identify evolutionary relationships through structural similarity among proteins.
• Protein function studies: Support investigation of protein function by providing accurate structural alignments.
• Structure-based drug design: Provide structural alignments that inform drug design efforts based on protein structural insights.

Methodology:

mTM-align applies a heuristic search algorithm and a hierarchical organization of the protein structure database for fast candidate retrieval, followed by the mTM-align algorithm for multiple-structure alignment to improve speed and accuracy relative to peer methods.