mdciao

mdciao analyzes and visualizes molecular dynamics (MD) simulation data with a focus on residue-residue contact frequencies and domain-specific annotations.

Key Features:

• Residue-residue contact frequency analysis: Computes and represents contact frequencies between residues from MD trajectories.
• Domain-specific annotations: Enriches analyses with annotations for GPCRs, GAIN-domains, G-proteins, and kinases through online lookups of generic residue numbering schemes.
• Cross-system comparison: Enables selection and comparison across different systems regardless of sequence identity, target residues, or domains.
• Automated figure and table generation: Produces annotated, production-ready figures and tables automatically.
• Python API: Provides programmatic access to basic and advanced functions for integration into analysis workflows.

Scientific Applications:

• GPCR analysis: Facilitates residue selection and comparison using generic GPCR residue numbering.
• GAIN-domain analysis: Supports annotation and analysis of GAIN-domain containing proteins via domain-specific numbering.
• G-protein analysis: Enables comparative studies of G-proteins using standardized residue nomenclature.
• Kinase analysis: Allows analysis and comparison of kinase structures and dynamics through generic kinase residue numbering.

Methodology:

mdciao computes residue-residue contact frequencies from MD simulation trajectories and performs online lookups of domain-specific generic residue numbering databases for annotation.