ICGEBnet Protein Tools

ICGEBnet Protein Tools provides quantitative analyses of three-dimensional protein structures to compute atomic protrusion (CX), depth (DPX), and fold-similarity (PRIDE) metrics for structural interpretation.

Key Features:

• Protrusion Index Calculation (CX): Centers a sphere of predetermined radius around each non-hydrogen atom to compute internal and external volumes and the CX ratio, reads PDB files, and writes CX values into the B-factor field for downstream analysis such as protein-protein complex assessment and proteolysis site prediction.
• Depth Index Calculation (DPX): Measures atom depth as the distance to the closest solvent-accessible atom by processing PDB files with atomic solvent accessibility information and writes DPX values into the B-factor field to analyze buried residue distribution and protein interior stability.
• Protein Fold Similarity Server (PRIDE): Compares structures using C(alpha)-C(alpha) distance histograms without structural alignment or secondary-structure assignment, computes a probability of identity (PRIDE score, 0–1) that correlates with C(alpha) RMSD, and enables efficient database scanning and fold classification with demonstrated accuracy on the CATH database.

Scientific Applications:

• Protein-Protein Interaction Analysis: CX identifies protruding regions to predict interaction sites and inform complex formation studies.
• Structural Stability Studies: DPX characterizes the distribution of buried residues to inform assessments of structural stability and functional site burial.
• Fold Recognition and Classification: PRIDE enables rapid fold recognition and classification to support studies of protein evolution and function prediction.

Methodology:

Standalone programs written in C read and write PDB files; CX computes internal/external volumes by centering a sphere around each non-hydrogen atom; DPX computes distances from each atom to the nearest solvent-accessible atom; PRIDE generates C(alpha)-C(alpha) distance histograms and computes a probability-of-identity score written as PRIDE output; computed indices are recorded in the PDB B-factor field.