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What is MCCE?

MCCE can calculate residue pka, cofactor Em and protein PI in protein-solvent systems. It is actually much more than that.

MCCE (Multi-Conformation Continuum Electrostatics) is a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics. MCCE can be used to study:

  • Protein structural responses to changes in charge;
  • Changes in charge state of ionizable residues due to structural changes in the protein;
  • The structural and ionization changes caused by changes in solution pH or Eh;
  • Find the location and stoichiometry of proton transfers coupled to electron transfer;
  • Make side chain rotomer packingpredictions as a function of pH.

Latest News:

  • February, 2008, support open to users via discussion forum.
  • August 4, 2006. The latest MCCE2.2 with some bug fixes is uploaded;
  • December 1, 2005: A Linux patch is available for downloads earlier than February, 2005. This patch fixes the boundary condition, and you only need it if you don't see "Step 3 dielectric boundary condition is corrected" in the program output. To apply the patch, just replace your mcce executable with the this program. Mac version is up to date.
  • February 17, 2005: A pKa benchmark was performed by matching the MCCE calculated pKas 179 unique residues in 44 structuctures of 14 proteins to the experimental pKas. The overall RMSD between the calculated and the measured is 0.77. The RMSD of buried half residues is 0.91 and the exposed half is 0.56. The prediction accuracy is 98% at error tolerance 2.0 pH units and 84% at error tolerance 1 pH unit.
  • This has corrections not found in the current release. If you registered by sending email to jmao@sci.ccny.cuny.edu or with the registration form we we send you the new release shortly.

    The pKa benchmark of calculated pKas (at dielectric constant 8) against measured pKas . The dashed lines represent 1 pH unit error tolerance.
  • September 15, 2004: MCCE2.0 Linux version is released.
  • NSFsupport for MCCE is gratefully acknowledged.