SS3D

SS3D integrates sequence and structural data to quantify spatial similarity between homologous protein residues within defined radii for comparative and functional analyses.

Key Features:

• Sequence and Structure Integration: Unifies sequence alignment with structure superposition to compare homologous proteins.
• Through-space Contact Identification: Identifies through-space contacts between residues of homologous proteins.
• Spatial Similarity Quantification: Quantifies spatial similarity by evaluating residues within a specified radius around homologous contacts.
• Scoring Mechanism: Employs native BLOSUM and PAM substitution matrices to score spatial alignments.
• Implementation: Developed in C++.
• Case Study Demonstrations: Applied to GPCR, p53, kelch, SUMO, and SARS coronavirus spike proteins to illustrate biologically significant regions of similarity and dissimilarity.

Scientific Applications:

• Conserved Position Identification: Pinpoints conserved positions across protein families by combining sequence and structural information.
• Functional Divergence Analysis: Highlights spatial differences that explain functional divergence among evolutionarily related proteins.
• Comparative Structural Studies: Enables nuanced comparisons of homologous proteins to investigate evolutionary relationships and structural adaptations.

Methodology:

SS3D identifies through-space contacts between residues and integrates sequence alignment with structure superposition; it then quantifies spatial similarity within a specified radius around those contacts using BLOSUM and PAM substitution matrices.