3DCOMB

3DCOMB generates multiple structure alignments (MSAs) for large sets of distantly related protein structures by integrating local and global structural information.

Key Features:

• Highly Similar Fragment Block Identification: Detects highly similar fragment blocks (HSFBs) by integrating local and global structural environments across protein structures.
• High-Quality Pairwise Structural Alignments: Produces accurate pairwise alignments that support construction of biologically meaningful multiple structure alignments.
• Non-Progressive Alignment Strategy: Extends alignments from identified HSFBs using a non-progressive method to efficiently generate MSAs for distantly related proteins.
• Functional Region Alignment: Aligns structurally diverse proteins while preserving functionally similar regions.

Scientific Applications:

• Multiple Template Homology Modeling: Supports improved template selection and alignment for multiple-template homology modeling of protein structures.
• Protein Structure Evolution Studies: Enables comparative structural analysis of distantly related proteins to investigate evolutionary relationships and functional conservation.

Methodology:

3DCOMB identifies highly similar fragment blocks using statistical learning applied to local and global structural environments, generates pairwise alignments, and extends these fragments using a non-progressive strategy to construct multiple structure alignments.