PKAD: a database of experimentally measured pKa values of ionizable groups in proteins

Database : the Journal of Biological Databases and Curation
Swagata PahariEmil Alexov

Abstract

Ionizable residues play key roles in many biological phenomena including protein folding, enzyme catalysis and binding. We present PKAD, a database of experimentally measured pKas of protein residues reported in the literature or taken from existing databases. The database contains pKa data for 1350 residues in 157 wild-type proteins and for 232 residues in 45 mutant proteins. Most of these values are for Asp, Glu, His and Lys amino acids. The database is available as downloadable file as well as a web server (http://compbio.clemson.edu/pkad). The PKAD database can be used as a benchmarking source for development and improvement of pKa's prediction methods. The web server provides additional information taken from the corresponding structures and amino acid sequences, which allows for easy search and grouping of the experimental pKas according to various biophysical characteristics, amino acid type and others.

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Citations

Mar 27, 2019·Drug Testing and Analysis·Markus ZilkerUlrike Holzgrabe
Dec 2, 2020·Journal of the Royal Society, Interface·Sheng-Ping LiangLior Sepunaru
Dec 5, 2020·Future Medicinal Chemistry·Elena De Vita
Dec 20, 2020·Journal of Inorganic Biochemistry·Kamila Stokowa-SołtysMałgorzata Jeżowska-Bojczuk
Apr 25, 2020·Journal of Chemical Theory and Computation·Robert C HarrisJana Shen
Apr 4, 2021·International Journal of Molecular Sciences·Giulia BabbiRita Casadio
Apr 28, 2021·Nucleic Acids Research·Lukasz Pawel Kozlowski
May 18, 2021·Journal of the American Chemical Society·Tinna PálmadóttirSara Linse
Jun 25, 2021·Journal of Chemical Theory and Computation·David J ReilleyAnastassia N Alexandrova
Jul 3, 2021·Membranes·Vanesa Viviana Galassi, Natalia Wilke
Jun 17, 2020·Journal of the American Society for Mass Spectrometry·Daniel W WoodallDavid E Clemmer
May 20, 2020·The Journal of Physical Chemistry. B·Laura Zanetti-PolziAndrea Amadei
Aug 29, 2020·Journal of Chemical Information and Modeling·Pedro B P S ReisMiguel Machuqueiro
Nov 28, 2021·Scientific Reports·Heyi ZhangHugo van Ingen
Nov 27, 2021·Biophysical Journal·Martin J FossatRohit V Pappu
Jul 15, 2021·Bioinformatics·Pedro B P S ReisMiguel Machuqueiro

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Methods Mentioned

BETA
protein folding
nuclear magnetic resonance
NMR
electrophoresis

Software Mentioned

MariaDB
NACCESS

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