|Introduction||Server||Electrostatic Potential||Signatures||Similarity & Clustering||Software||Results||References|
2. Electrostatic Potential
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)