Experimental data for the SAMPL5 Cyclohexane/Water Log D challenge
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Manuscript
bootstrap_code
docs
raw_data
.gitattributes
README.md
analysis.py
logD_final.txt
processed.xlsx

README.md

SAMPL5 Distribution coefficients

Authors

  • Bas Rustenburg
    • Genentech, South San Francisco, CA
    • Memorial Sloan Kettering, New York, NY // Chodera Lab
  • John Chodera
    • Memorial Sloan Kettering, New York, NY
  • David Mobley
    • University of California, Irvine, Irvine, CA

Description

As part of the SAMPL5 challenge, cyclohexane-water distribution coefficients (Log D) have been measured at Genentech for 53 small, drug-like molecules. The technique used is a mass spectrometry-based assay as described in Lin & Pease, 2013.

Inside this repository you will find raw and processed data files containing the experimental data that was collected, the final results as well as the python scripts used to analyze the data.

Files

See Manuscript for all files used to generate figures and tables for the manuscript.

See bootstrap_code/bootstrap_model.py for our bootstrap analysis code.

See logD_final.txt for final data values, generated by analysis.py.

The experimental data that was used for the analysis is found in processed.xlsx.

Additionally, unprocessed, raw data files, as well as processing scripts are found in raw_data.

See docs for a documentation of the analysis.

Acknowledgements

  • Dan Ortwine, Genentech
  • Baiwei Lin, Genentech
  • Joseph Pease, Genentech
  • Justin Dancer, Genentech
  • JW Feng, Denali Therapeutics
  • Caitlin Bannan, University of California, Irvine // Mobley Lab