espsim 1.0 (zip)

Release notes:

ESPSim is an open source JAVA application designed to compute the similiraity of protein electrostatic potential maps.  ESPSim may be of use to those studying the conservation of protein electrostatic properties as well as in determining the effects of mutations on a proteins electrostatic potential surface. 

Steps for Using ESPSim

1)      Select your PDB structures of interest and align them using a program such as Swiss PDB Viewer or Pymol.

2)      Perform electrostatic calculations using APBS or similar program, being certain to use consistent grid dimensions and spacing for each computation.

3)      From your calculation output, select your grid points of interest and convert the data into the format used by ESPSim- a listing of:

 

X Coordinate₁    Y Coordinate₁    Z Coordinate₁    Electrostatic Potential₁

.                               .                               .                               .

.                               .                               .                               .

.                               .                               .                               .

X Coordinate_n    Y Coordinate_n    Z Coordinate_n    Electrostatic Potential_n

 

for each point to be included in the calculation.

4)      Load two files containing the electrostatic potential data and click Calculate Similarity.

 

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Changelog: