POPSCOMP

POPSCOMP calculates buried molecular surface areas in biomolecular complexes to quantify interaction surfaces between proteins, DNA, and RNA and to support analysis of residue-level contacts and interaction energies.

Key Features:

• Interaction Surface Calculation: Calculates the interaction surface between complex components (proteins, DNA, RNA) by quantifying molecular surface area rendered inaccessible upon complex formation.
• Data Output: Produces matrices and graphs representing buried surface areas for annotation of interacting components and residues, visualization of conformational changes, and estimation of interaction energies.
• Resolution Flexibility: Performs analyses at per-atom resolution for high-resolution structures or at per-residue resolution for lower-resolution data.
• Automated Analysis: Automates batch analysis to process large datasets and extract interaction annotations without manual per-complex calculations.

Scientific Applications:

• Ribosome–antibiotic interactions: Maps residues involved in ribosomal binding and conformational changes in ribosome–antibiotic complexes to inform mechanisms of antibiotic action.
• Structural biology and pharmacology: Estimates interaction energies and buried surface metrics to support structural biology studies and pharmacological evaluation of drug targets.

Methodology:

Computationally compares structures to determine buried surface area upon complex formation, outputs matrices and graphs of buried areas, and annotates interacting components and residues through automated calculations.