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:
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.