PCE: Protein Continuum Electrostatics

PCE performs the calculation of the electrostatic potentials for a protein by solving numerically the Poisson-Boltzmann equation (the Finite Difference Poisson- Boltzmann method, FDPB). It is a server adaptation of the MEAD potential program (MEAD: Macroscopic Electrostatics with Atomic Detail, D. Bashford).

Two types of services are currently proposed: electrostatic potentials calculation and pKa calculations.

Access the services:
PCE-pot
PCE-pKa


More information:


PCE potentials calculated with MEAD Input:
When using a PDB file as input, the current version assumes that GLU, ASP, C-term are charged negatively and ARG, LYS, N-term are charged positively. Partial charges (PARSE parameters; Sitkoff et al. 1994 J Phys Chem 98, 1978-88) are assigned on all atoms.

Warnings:
- Starting from a PDB file as input, this service currently takes into account only protein atoms but work is in progress to consider hetero-atoms.
- A pdb file could include a number of protein structures (like many NMR structures), thus be sure you select the appropriate structure, with regard to NMR file, at present, only the first structure will be considered.

Calculation parameters:

Results:


 PCE pKa calculations with MEAD

PCE performs calculations of the pKa values of titratable groups in proteins.This approach implies calculation of the intrinsic pKa values of all titratable groups (defined as the pKa of one titratable group if all other titratable groups in the protein were held in their neutral forms), as well as the pair-wise electrostatic interactions between the titratable groups. PARSE parameters are used in the present version of PCE.

Input:
Warning: A pdb file could include a number of protein structures (like many NMR structures), thus be sure you select the appropriate structure, with regard to NMR file, at present, only the first structure will be considered.

Calculation parameters:
Output file: