Bios2cor

Bios2cor integrates dynamic correlations from molecular dynamics (MD) simulations and evolutionary correlations from multiple sequence alignments (MSAs) as an R package to identify residues critical for protein function.

Key Features:

• Integration of dynamic and evolutionary data: Combines sidechain motion correlations from MD simulations with evolutionary covariation derived from MSAs to analyze residue relationships.
• Correlation/covariation score computation: Computes correlation or covariation scores between positions within an MSA and between sidechain dihedral angles or rotamers in MD trajectories.
• Analytical, visualization, and interpretation tools: Provides analysis, visualization, and interpretation capabilities for correlation data to support residue-level functional inferences.

Scientific Applications:

• Structure–function analysis: Identifies residues whose combined dynamic and evolutionary correlations implicate roles in protein function and mechanism.
• Stability and interaction-site analysis: Highlights residues that may influence protein stability or mediate interaction sites via correlated motions and conservation patterns.
• Drug target and functional residue identification: Pinpoints candidate residues for functional perturbation or drug design based on combined dynamic and evolutionary signals.

Methodology:

Operates on either an MSA or an MD trajectory as input, computes correlation/covariation scores between MSA positions or MD sidechain dihedral angles/rotamers, and performs analysis and visualization of the resulting correlation data.