Patch Finder Plus Manual
Input
PDB Selection: Patch Finder Plus requires a coordinate file in PDB format. The input can be given in one of two ways:
  • Supply a valid PDB ID (a 4 character alphanumeric identifier). In this case Patch Finder will download the file from RCSB PDB.
  • Upload a user-defined coordinate file (of a known structure or a model) in PDB format.
Chain Selection: By default, the calculation is performed on all the protein chains (each protein chain is calculated separately). However, it is possible to select a specific chain identifier. In such case, only the selected chain will be calculated and displayed in the results (this option is recommended when you have a specific chain of interest, to reduce the calculation time).
Results
An example of Patch Finder Plus output file:
output_example
In cases the calculation is performed on several protein chains, the first protein chain is initially displayed. The displayed results can be changed to each of the protein chains by using the drop-down menu in the title.
Graphic display: Patch Finder Plus visualizes the largest positive patch on the protein surface using Jmol viewer (an interactive java-based web browser applet). In order to display the protein properly, make sure you have Java installed on your computer and that your browser enables Java applets (For more information: How do I enable Java in my web browser?).
The largest positive patch is colored blue, as in the picture above.
Output files: Patch Finder Plus creates two output files that can be downloaded by the user.
  • A list of the residues composing each patch.
  • The Jmol script used by Patch Finder to display the three largest positive patches in Jmol viewer.
    If you want to display the protein in any other visualization program (Chimera, Pymol, etc.), you should translate the Jmol script to the desired program syntax.
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]