Published June 24, 2021 | Version 0.1
Dataset Open

pKaDatabase for Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge

Authors/Creators

  • 1. Temple University

Description

A curated a database of small molecules with experimentally measured pKa values. 

This pickle file can be loaded into memory using Pandas. In the code block below we will print out the columns of the DataFrame:

import pandas as pd
df = pd.load("pKaDatabase.pkl")
print(df.keys()). # print the columns

['deprotonated microstate ID', 'protonated microstate ID', 'deprotonated microstate smiles', 'protonated microstate smiles', 'AM1BCC partial charge (prot. atom)', 'AM1BCC partial charge (deprot. atom)', 'AM1BCC partial charge (prot. atoms 1 bond away)', 'AM1BCC partial charge (deprot. atoms 1 bond away)', 'AM1BCC partial charge (prot. atoms 2 bond away)', 'AM1BCC partial charge (deprot. atoms 2 bond away)', 'Gasteiger partial charge (prot. atom)', 'Gasteiger partial charge (deprot. atom)', 'Gasteiger partial charge (prot. atoms 1 bond away)', 'Gasteiger partial charge (deprot. atoms 1 bond away)', 'Gasteiger partial charge (prot. atoms 2 bond away)', 'Gasteiger partial charge (deprot. atoms 2 bond away)', 'Extented Hückel partial charge (prot. atom)', 'Extented Hückel partial charge (deprot. atom)', 'Extented Hückel partial charge (prot. atoms 1 bond away)', 'Extented Hückel partial charge (deprot. atoms 1 bond away)', 'Extented Hückel partial charge (prot. atoms 2 bond away)', 'Extented Hückel partial charge (deprot. atoms 2 bond away)', '∆G_solv (kJ/mol) (prot-deprot)', 'SASA (Shrake)', 'SASA (Lee)', 'Bond Order', 'Change in Enthalpy (kJ/mol) (prot-deprot)', 'pKa','href', 'num ionizable groups', 'Weight', 'pKa source']

 

For more information regarding feature calculations, please read the following paper:

Raddi, Robert, and Vincent Voelz. "Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge." (2021). 10.26434/chemrxiv.14650302.v1

Notes

Funding: National Institute of General Medical Sciences (R01GM123296)

Files

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Additional details

Related works

Cites
Dataset: 10.1007/s10822-011-9440-2 (DOI)
Is supplement to
Journal article: 10.26434/chemrxiv.14650302.v1 (DOI)

References

  • Raddi, R., & Voelz, V. (2021). Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge.
  • Sushko, I., Novotarskyi, S., Körner, R., Pandey, A. K., Rupp, M., Teetz, W., ... & Tetko, I. V. (2011). Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. Journal of computer-aided molecular design, 25(6), 533-554.
  • Caine, B. A., Bronzato, M., & Popelier, P. L. (2019). Experiment stands corrected: accurate prediction of the aqueous p K a values of sulfonamide drugs using equilibrium bond lengths. Chemical science, 10(25), 6368-6381.
  • Settimo, L., Bellman, K., & Knegtel, R. M. (2014). Comparison of the accuracy of experimental and predicted pKa values of basic and acidic compounds. Pharmaceutical research, 31(4), 1082-1095.