PFP

PFP identifies continuous electrostatic positive patches on protein surfaces to locate putative nucleic acid binding interfaces and other functionally relevant electrostatic regions.

Key Features:

• Input formats: Accepts a four-letter Protein Data Bank (PDB) code or a coordinate file in PDB format as input.
• Continuum electrostatics: Computes the continuum electrostatics potential of the provided protein structure.
• Patch extraction: Extracts the largest contiguous positive patch for each chain present in the input file.
• Electrostatic distribution analysis: Analyzes the electrostatic potential distribution across the protein surface to identify extensive positive regions.
• Residue-level output: Produces a downloadable PDB-format output file listing the residues that constitute each identified positive patch.
• Visualization: Generates an interactive graphical display of the largest positive patch using Jmol with color coding for interpretation.
• Scope of detection: Detects significant positive surface areas in proteins irrespective of known nucleic acid-binding function, enabling investigation of other family-specific functional properties.

Scientific Applications:

• Nucleic acid interaction mapping: Identification of putative nucleic acid binding interfaces on protein surfaces.
• Structure–function analysis: Exploration of relationships between electrostatic surface properties and protein functional roles.
• Comparative family studies: Detection of conserved or family-specific positive surface regions for functional hypothesis generation.
• Drug discovery and biotechnology: Use of electrostatic patch information to inform target site selection and protein engineering strategies.

Methodology:

Computes the continuum electrostatics potential of the input PDB structure, analyzes the electrostatic potential distribution to extract the largest contiguous positive patch for each chain, outputs a PDB file listing patch residues, and produces a Jmol-based graphical display.