CRASP

CRASP analyzes multiple sequence alignments of amino acid sequences to detect coordinated residue substitutions and infer co-evolutionary relationships between protein sites.

Key Features:

• Coordinated Substitution Detection: Identifies correlated amino acid substitutions occurring at interacting positions within protein sequences.
• Correlation-Based Analysis: Estimates correlation coefficients between physicochemical parameters at pairs of alignment positions to detect functional dependencies.
• Physicochemical Property Evaluation: Examines coordinated substitutions affecting parameters such as net charge and hydrophobic core volume.
• Pairwise Residue Relationship Analysis: Analyzes pairwise substitution relationships between amino acid positions in multiple sequence alignments.

Scientific Applications:

• Protein Co-evolution Analysis: Identifies co-evolving amino acid residues involved in structural or functional interactions.
• Protein Structure–Function Studies: Supports investigation of residue dependencies influencing protein stability and activity.
• Molecular Evolution Research: Enables analysis of evolutionary constraints shaping substitution patterns in protein sequences.

Methodology:

CRASP analyzes multiple sequence alignments and calculates correlation coefficients between physicochemical properties of amino acids at aligned positions to identify coordinated residue substitutions.