Surfnet




Automated cleft calculation.


Surface and void region detection.

ebisu group

chemogenomix © 2012

Read more below

Overview

Surfnet was developed to calculate cleft, surfaces and void regions in proteins. It is a fairly simple program run from a parameter file.

It is also use as a component of PDBsumProprietary


Data Input

Data input is from coordinate files the obey the PDB format.


Running the software

When Surfnet is run, output is written to an .srf file.

This .srf file can then be processed by the supporting tools to compare different sites.

For visualisation a .den density file or VRML can be generated.

The .den files can be read directly by some 3rd party programs or indirectly using converter programs available in the CCP4 package.

Though one of the older programs in our portfolio, it works well.


Availability

Linux  Can run on virtual machine.

For more information on how this program might be used download the pdf of our original paper by simply clicking on the image. Or see this more recent 2006 publication here