Short project description
Karlsberg2+ (previous version Karlsberg+) is a software performing pKa predictions of ionizable residues in any protein provided. It combines continuum electrostatics with structural relaxation of hydrogens and salt bridges. Starting from the user supplied structure Karlsberg2+ will 'predict' hydrogen positions and alternative side chain conformers for ion pairs present in salt bridges depending on the bulk pH. After evaluating the relevant electrostatic energies Karlsberg2+ performs a Monte-Carlo sampling of protein protonation patterns and the predicted pH adapted conformations. The approach has been shown to increase the accuracy of LPBE-based pKas without meddling with the protein dielectric constant for which Karlsberg2+ uses a consistent value of 4.0.


Karlsberg2+ package is in preparation. Software files and setup instructions are available on request.