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

2019 Database: The Journal of Biological Databases and Curation  
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.  ...  Funding National Institutes of Health (R01GM093937). Conflict of interest. None declared.  ... 
doi:10.1093/database/baz024 pmid:30805645 pmcid:PMC6389863 fatcat:k7igthz2cjdnjmexwaxzjylvqu

Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1.0]

Shailesh Kumar Panday, Mihiri H.B. Shashikala, Mahesh Koirala, Swagata Pahari, Arghya Chakrvorty, Yunhui Peng, Lin Li, Zhe Jia, Chuan Li, Emil Alexov
2019 Living journal of computational molecular science  
PKAD PKAD is a database of experimentally measured pKa values of titratable residues in proteins.  ...  RES ID: The residue ID number of the corresponding residue, whose pKa values are to be measured. Expt. pKa: Experimentally measured pKa values of each protein residue. Expt.  ...  DelPhiPKa DelPhiPKa [22] is a DelPhi based C++ program, which predicts the pKa's of ionizable and polar groups in proteins, DNA and RNAs.  ... 
doi:10.33011/livecoms.1.2.10841 fatcat:5t5rrwvutvhxjjjka2d4tubyga

Prediction of Protein pKa with Representation Learning

Hatice Hatice Gokcan, Olexandr Isayev
2022 Chemical Science  
The behavior of proteins is closely related to the protonation states of the residues. Therefore, prediction and measurement of pKa are essential to understand the basic functions of proteins. In...  ...  This publication resulted in part from research supported by the Office of Naval Research (ONR) through the Energetic Materials Program (MURI grant no. N00014-21-1-2476).  ...  This research is part of the Frontera computing project at the Texas Advanced Computing Center. Frontera is made possible by the National Science Foundation award OAC-1818253.  ... 
doi:10.1039/d1sc05610g pmid:35310485 pmcid:PMC8864681 fatcat:j6xo454pijf75fbimrj622ykgm

The pH-dependent gating of the human voltage-gated proton channel from computational simulations

Christophe Jardin, Niklas Ohlwein, Arne Franzen, Gustavo Chaves, Boris Musset
2022
Therefore, the pKa of every titratable amino acids has been assessed in single simulations.  ...  Despite experimental investigations to identify the amino acids involved in pH sensing only few progress has been made, including one histidine at the cytoplasmic side of the channel that is involved in  ...  The 'standard' values are (a) from the PKAD database based on experimentally measured pK a s of 1350 ionizable AAs in 157 wild-type proteins (408 Asp, 4177 Glu, 253 His, and 155 Lys), 58 (b) the values  ... 
doi:10.1039/d1cp05609c pmid:35445675 fatcat:f56drsrajbcejmjqhbbvfmue7a