PASS2

PASS2 provides structure-based sequence alignments of protein domain superfamilies to identify conserved structural and functional features for evolutionary and functional analysis.

Key Features:

• Structure-Based Sequence Alignments: Generates alignments based on three-dimensional structures rather than primary sequences to identify conserved features in proteins with low sequence similarity.
• Comprehensive Coverage: Encompasses 1,961 superfamilies and 10,569 protein domains to represent known structural domain superfamilies.
• Correspondence with SCOP Database: Is aligned with the Structural Classification of Proteins (SCOP) version 1.75 for standardized classification and comparison.
• Automated Updates: Features an automated update mechanism for periodic refresh of database entries and associated data.
• Efficient Alignment Methods: Employs improved methods to enhance efficiency of structure-based sequence alignments, especially for extremely distantly related proteins within superfamilies.
• Functional Residue Analysis: Enables alignment of family-specific functional residues to support comparative analysis of functional sites across superfamily members.

Scientific Applications:

• Protein Domain Research: Exploration of evolutionary relationships and structural conservation among proteins within superfamilies.
• Functional Annotation: Alignment of functional residues to assist annotation of unknown protein functions based on known structures.
• Structural Biology Studies: Support for analyses of protein domain architecture and dynamics through detailed structure-based alignments.

Methodology:

Employs advanced computational techniques to generate structure-based sequence alignments by leveraging three-dimensional structural data to align distantly related proteins within common superfamilies.