Electrostatic Potential

2. Electrostatic Potential

Protein Data

1415 Protein subset from protein Data Bank (PDB) were parameterized into formats acceptable for subsequent electrostatics calculations.

Calculation of Electrostatic Potential

APBS software (N. Baker, Holst, and McCammon research groups)

  • Solves PBE with efficient multilevel finite difference and finite element algorithms
  • Trivially parallel APBS Grid Portal (J. Greenberg, SDSC and McCammon research group)
  • Provides web-based user access to NPACI resources
  • Facilitates job submission and management
  • Uses Storage Resource Broker (SRB) for uniform data access

Isosurface of Electrostatics potential and rendered as a function on an isosurface of electron density (electrostatics data courtesy Dr. Nathan Baker, Washington University in St. Louis).
blue:positive white:neutral red:negative

Images generated by Volume Rover

Electrostatic Potential Visualization of Ribosome Large Subunit (1JJ2)

Red-Negative, Blue-Positive, White-Neutral