What is pKa database?

pKa database is intended to host known pKa values from experiment measurement as well as theoretical calculations. Protein residue pKas are a measure of protonation capability of residues and the knowledge helps solving many problems such as protein folding, protein binding, and protein catalytic mechanisms.

Our current research interest of using this database is to understand the energy conversion through proton transfer in photosynthetic proteins. Besides the experimental pKas, we use primarily MCCE as our theoretical method to obtain pKas wherever a directly measured pKa is not available.

The description of MCCE method can be found on:
Journal of Computational Chemistry Volume 30, Issue 14, Pages 2231-2247

pKa entries growth

pKa database news

• 07/18/2011 MCCE gfortran source code is available (Works on Mac and Linux).source code
• 06/09/2011 Uploding 4800 structures calculated by MCCE at dielectric constant 8. These are not official results.
• 02/20/2011 Identified 10895 protein structures for pKa calculation candidates.link
• 12/2/2009 pKa database growth plotting function is added.
• 11/25/2009 700 Experimental pKa values are uploaded to the database.
• 11/24/2009 Server pKa.engr.ccny.cuny.edu is up.