Algorithm Overview
Patch Finder Plus is an automatic server to extract and display the largest positive electrostatic patch on a protein surface. The algorithm automatically assigns surface positive patches by looking for adjacent points on the protein surface that meet a given electrostatic potential cutoff. In the current version of Patch Finder Plus, the potential cutoff is fixed to 2 kT/e.
The algorithm is built of five major steps:
  1. Calculating the electrostatic potential of the protein on a three dimensional grid, using the Poisson Boltzmann equation.
  2. Defining the grid points that fall closest to the protein surface while emitting all non surface points.
  3. Extracting all three-dimensional patches of adjacent grid points which meet the defined cutoff.
  4. Choosing the largest positive patch for each protein chain.
  5. Assigning the protein residues related to the patch.
As a preparation step for the electrostatic calculation, hydrogen atoms are assigned to the structure using the PDB2PQR package.
The electrostatic potential is calculated using the APBS software. The grid spacing is set to 1Å and the rest of the parameters are set to default.
The molecular surface is computed using the open source program DMS.
Reference:
  • Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, Yael Mandel-Gutfreund (2007) Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Res., 35:526-30. [PDF]