Merge pull request #73 from MobleyLab/logP_experimental_data

Release logP experimental data for SAMPL6 logP challenge.
samplchallenges · Mar 25, 2019 · 37d148d · 37d148d
2 parents 964375f + 59cdd35
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diff --git a/README.md b/README.md
@@ -48,6 +48,7 @@ The SAMPL project was recently funded by the National Institutes of Health, for
 - Version 1.12: Update of the SAMPLing analysis.
 - Version 1.13: SAMPL6 Part II - Instructions for log *P* challenge posted.
 - Version 1.14: SAMPL6 Part II - Announcement that log *P* challenge submissions opened. Instructions on how to submit prediction files through D3R SAMPL webpage added to log *P* challenge instructions.
+- Version 1.15: SAMPL6 Part II - Include experimental measurements for the log *P* challenge.
 
 ### Changes not yet in a release
 
@@ -120,6 +121,8 @@ Challenge submissions due: Mar 22, 2019
 
 Detailed instructions for the logP challenge can be found here: [logP_challenge_instructions.md](logP_challenge_instructions.md)
 
+Experimental log *P* measurements were added to this repository after the log *P* challenge deadline and can be found here: [physical_properties/logP/experimental_data/](physical_properties/logP/experimental_data/)
+
 ### SAMPLing challenge
 The purpose of the SAMPLing challenge component is to evaluate and compare the performance of different sampling methodologies in the context of free energy calculations of biomolecular systems. Participants are invited to compute the free energy of binding of few host-guest systems taken from the main SAMPL6 challenge. We will be running extremely long calculations with the provided input files in an attempt to obtain "gold standard" results, and then assess how well different methods approach/converge to these results. See [`SAMPLing_instructions.md`](SAMPLing_instructions.md) for more details.
 

diff --git a/physical_properties/README.md b/physical_properties/README.md
@@ -22,5 +22,6 @@ For detailed instructions for log *P* challenge: [SAMPL6/logP_challenge_instruct
 Challenge start date: Nov 1, 2018  
 Challenge submission due: Mar 22, 2019  
 
+Experimental log *P* measurements were added to this repository after the log *P* challenge deadline and can be found here: [logP/experimental_data/](logP/experimental_data/)
 
 
diff --git a/physical_properties/logP/README.md b/physical_properties/logP/README.md
@@ -19,3 +19,4 @@ Experimental log *P* measurements will be made available in this repository afte
 - `/submission_template/logP_prediction_template.csv` - An empty prediction submission template files.
 -  `/example_submission_file/logP-MehtapIsikExampleFile-1.csv` - An example submission file filled with random values to illustrate expected format.
 - `/example_experimental_data/` - This directory contains the experimental report of pH-metric log *P* measurement of phenol with Sirius T3 as an example.
+- `/experimental_data/` - Experimental measurements of log *P* values.
diff --git a/physical_properties/logP/experimental_data/README.md b/physical_properties/logP/experimental_data/README.md
@@ -0,0 +1,27 @@
+## Experimental log *P* values of SAMPL6 Part II log *P* challenge molecules
+
+This directory contains the results of the log *P* measurements for 11 small molecules of SAMPL6 Part II log *P* challenge. 
+
+Experimental log *P* values were collected using potentiometric (pH-metric log *P*) measurements with a Sirius T3 instrument by Mehtap Isik from the Chodera Lab at MSKCC with the support of the Preformulation Group, Pharmaceutical Sciences, MRL, Merck & Co., Inc, especially Dorothy Levorse, Timothy Rhodes, and Brad Sherborne.
+
+A minimum of 3 independent replicates of log *P* measurements were done for each molecule. 
+Please see [SAMPL6/logP Challenge Instructions/Experimental Details](https://github.com/MobleyLab/SAMPL6/blob/master/logP_challenge_instructions.md#experimental-details) for more details about the experimental method.
+
+The mean and standard error of the mean(SEM) of experimental octanol-water log *P* values were reported in `logP_experimental_values.csv` file, calculated as
+
+![mean_and_SEM_calculation.png](mean_and_SEM_calculation.png)
+
+The same batches of compounds as the pKa measurements for SAMPL6 pKa challenge were used for log *P* measurements. So, for purity information of analytes refer to [`SAMPL6/physical_properties/pKa/experimental_data/purity/` directory](https://github.com/MobleyLab/SAMPL6/blob/master/physical_properties/pKa/experimental_data/purity/purity_of_SAMPL6_pKa_compounds_determined_by_LCMS.csv).
+
+Aqueous pKa values of log *P* challenge compounds were previously determined using UV-metric measurements with the Sirius T3, as described in [the SAMPL6 pKa challenge](https://github.com/MobleyLab/SAMPL6/tree/logP_experimental_data/physical_properties/pKa). 
+These values were used as input for pH-metric log *P* measurements. 
+
+## Manifest
+
+- `logP_experimental_values.csv` - Mean and SEM of experimental log *P* values organized in a table for each molecule.
+- `logP_results_of_replicate_experiments.csv` - A table that contains experimental results of replicate log *P* measurements (N=3 or 4) and names of experimental reports (PDF files can be found in [`experiment_reports\` directory](https://github.com/MobleyLab/SAMPL6/tree/logP_experimental_data/physical_properties/logP/experimental_data/experiment_reports)).
+- `experiment_reports/` - This directory contains reports generated by Sirius T3 software for the results of log *P* measurements. Refer to `logP_results_of_replicate_experiments.csv` for matching SAMPL6 molecule IDs to names of the report files.
+- `experimental_ID_and_SAMPL6_molecule_ID_table.csv` - A table that matches experimental molecule IDs to SAMPL6 challenge molecule IDs.
+
+
+
diff --git a/...imental_data/experiment_reports/SM02_18C-01011_M02_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM02_18C-01011_M02_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM02_18C-03011_M02_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM02_18C-03011_M02_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM02_18C-03012_M02_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM02_18C-03012_M02_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM02_18C-06015_M02_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM02_18C-06015_M02_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM04_18C-24002_M04_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM04_18C-24002_M04_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM04_18C-24003_M04_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM04_18C-24003_M04_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM04_18C-24004_M04_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM04_18C-24004_M04_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM07_18B-28011_M07_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM07_18B-28011_M07_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM07_18B-28012_M07_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM07_18B-28012_M07_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM07_18B-28013_M07_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM07_18B-28013_M07_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM08_18C-02007_M08_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM08_18C-02007_M08_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM08_18C-02008_M08_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM08_18C-02008_M08_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM08_18C-02009_M08_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM08_18C-02009_M08_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM09_18C-02010_M09_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM09_18C-02010_M09_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM09_18C-03001_M09_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM09_18C-03001_M09_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM09_18C-06007_M09_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM09_18C-06007_M09_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM11_18B-27016_M11_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM11_18B-27016_M11_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM11_18C-01001_M11_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM11_18C-01001_M11_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM11_18C-01002_M11_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM11_18C-01002_M11_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM11_18C-09010_M11_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM11_18C-09010_M11_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM12_18C-01012_M12_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM12_18C-01012_M12_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM12_18C-03013_M12_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM12_18C-03013_M12_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM12_18C-03014_M12_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM12_18C-03014_M12_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM12_18C-03015_M12_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM12_18C-03015_M12_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM13_18C-09011_M13_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM13_18C-09011_M13_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM13_18C-16016_M13_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM13_18C-16016_M13_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM13_18C-26010_M13_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM13_18C-26010_M13_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM14_18B-28002_M15_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM14_18B-28002_M15_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM14_18C-01004_M15_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM14_18C-01004_M15_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM14_18C-01005_M15_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM14_18C-01005_M15_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM14_18C-03006_M15_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM14_18C-03006_M15_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM15_18C-01007_M16_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM15_18C-01007_M16_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM15_18C-01008_M16_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM15_18C-01008_M16_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM15_18C-01009_M16_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM15_18C-01009_M16_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM16_18C-09014_M18_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM16_18C-09014_M18_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM16_18C-09015_M18_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM16_18C-09015_M18_octanol_pH-metric high logP_report.pdf
diff --git a/...imental_data/experiment_reports/SM16_18C-09016_M18_octanol_pH-metric high logP_report.pdf b/...imental_data/experiment_reports/SM16_18C-09016_M18_octanol_pH-metric high logP_report.pdf
diff --git a/physical_properties/logP/experimental_data/experimental_ID_and_SAMPL6_molecule_ID_table.csv b/physical_properties/logP/experimental_data/experimental_ID_and_SAMPL6_molecule_ID_table.csv
@@ -0,0 +1,12 @@
+Experimental Molecule ID,SAMPL6 Molecule ID
+M02,SM02
+M04,SM04
+M07,SM07
+M08,SM08
+M09,SM09
+M11,SM11
+M12,SM12
+M13,SM13
+M15,SM14
+M16,SM15
+M18,SM16
diff --git a/physical_properties/logP/experimental_data/logP_experimental_values.csv b/physical_properties/logP/experimental_data/logP_experimental_values.csv
@@ -0,0 +1,12 @@
+Molecule ID,logP mean,logP SEM,Assay Type,Experimental ID,Isomeric SMILES
+SM02,4.09,0.03,pH-metric octanol logP,M02,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)C(F)(F)F
+SM04,3.98,0.03,pH-metric octanol logP,M04,c1ccc2c(c1)c(ncn2)NCc3ccc(cc3)Cl
+SM07,3.21,0.04,pH-metric octanol logP,M07,c1ccc(cc1)CNc2c3ccccc3ncn2
+SM08,3.10,0.03,pH-metric octanol logP (predose 80 uL octanol),M08,Cc1ccc2c(c1)c(c(c(=O)[nH]2)CC(=O)O)c3ccccc3
+SM09,3.03,0.07,pH-metric octanol logP,M09,COc1cccc(c1)Nc2c3ccccc3ncn2.Cl
+SM11,2.10,0.04,pH-metric octanol logP,M11,c1ccc(cc1)n2c3c(cn2)c(ncn3)N
+SM12,3.83,0.03,pH-metric octanol logP,M12,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)Cl.Cl
+SM13,2.92,0.04,pH-metric octanol logP (predose 100 uL octanol),M13,Cc1cccc(c1)Nc2c3cc(c(cc3ncn2)OC)OC
+SM14,1.95,0.03,pH-metric octanol logP,M15,c1ccc(cc1)n2cnc3c2ccc(c3)N
+SM15,3.07,0.03,pH-metric octanol logP,M16,c1ccc2c(c1)ncn2c3ccc(cc3)O
+SM16,2.62,0.01,pH-metric octanol logP (predose 100 uL octanol),M18,c1cc(c(c(c1)Cl)C(=O)Nc2ccncc2)Cl
diff --git a/physical_properties/logP/experimental_data/logP_results_of_replicate_experiments.csv b/physical_properties/logP/experimental_data/logP_results_of_replicate_experiments.csv
@@ -0,0 +1,38 @@
+Molecule ID,"logP, neutral","logP std, neutral",Assay Type,Experimental Molecule ID,Experiment ID,Isomeric SMILES,Experiment Report
+SM02,4.10,0.03,pH-metric octanol logP,M02,18C-01011,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)C(F)(F)F,SM02_18C-01011_M02_octanol_pH-metric high logP_report.pdf
+SM02,4.08,0.01,pH-metric octanol logP,M02,18C-03011,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)C(F)(F)F,SM02_18C-03011_M02_octanol_pH-metric high logP_report.pdf
+SM02,4.03,0.01,pH-metric octanol logP,M02,18C-03012,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)C(F)(F)F,SM02_18C-03012_M02_octanol_pH-metric high logP_report.pdf
+SM02,4.16,0.01,pH-metric octanol logP,M02,18C-06015,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)C(F)(F)F,SM02_18C-06015_M02_octanol_pH-metric high logP_report.pdf
+SM04,4.04,0.02,pH-metric octanol logP,M04,18C-24002,c1ccc2c(c1)c(ncn2)NCc3ccc(cc3)Cl,SM04_18C-24002_M04_octanol_pH-metric high logP_report.pdf
+SM04,3.95,0.01,pH-metric octanol logP,M04,18C-24003,c1ccc2c(c1)c(ncn2)NCc3ccc(cc3)Cl,SM04_18C-24003_M04_octanol_pH-metric high logP_report.pdf
+SM04,3.95,0.02,pH-metric octanol logP,M04,18C-24004,c1ccc2c(c1)c(ncn2)NCc3ccc(cc3)Cl,SM04_18C-24004_M04_octanol_pH-metric high logP_report.pdf
+SM07,3.29,0.01,pH-metric octanol logP,M07,18B-28011,c1ccc(cc1)CNc2c3ccccc3ncn2,SM07_18B-28011_M07_octanol_pH-metric high logP_report.pdf
+SM07,3.14,0.01,pH-metric octanol logP,M07,18B-28012,c1ccc(cc1)CNc2c3ccccc3ncn2,SM07_18B-28012_M07_octanol_pH-metric high logP_report.pdf
+SM07,3.21,0.01,pH-metric octanol logP,M07,18B-28013,c1ccc(cc1)CNc2c3ccccc3ncn2,SM07_18B-28013_M07_octanol_pH-metric high logP_report.pdf
+SM08,3.05,0.01,pH-metric octanol logP (predose 80 uL octanol),M08,18C-02007,Cc1ccc2c(c1)c(c(c(=O)[nH]2)CC(=O)O)c3ccccc3,SM08_18C-02007_M08_octanol_pH-metric high logP_report.pdf
+SM08,3.08,0.01,pH-metric octanol logP (predose 80 uL octanol),M08,18C-02008,Cc1ccc2c(c1)c(c(c(=O)[nH]2)CC(=O)O)c3ccccc3,SM08_18C-02008_M08_octanol_pH-metric high logP_report.pdf
+SM08,3.16,0.01,pH-metric octanol logP (predose 80 uL octanol),M08,18C-02009,Cc1ccc2c(c1)c(c(c(=O)[nH]2)CC(=O)O)c3ccccc3,SM08_18C-02009_M08_octanol_pH-metric high logP_report.pdf
+SM09,2.90,0.01,pH-metric octanol logP,M09,18C-02010,COc1cccc(c1)Nc2c3ccccc3ncn2.Cl,SM09_18C-02010_M09_octanol_pH-metric high logP_report.pdf
+SM09,3.14,0.01,pH-metric octanol logP,M09,18C-03001,COc1cccc(c1)Nc2c3ccccc3ncn2.Cl,SM09_18C-03001_M09_octanol_pH-metric high logP_report.pdf
+SM09,3.05,0.02,pH-metric octanol logP,M09,18C-06007,COc1cccc(c1)Nc2c3ccccc3ncn2.Cl,SM09_18C-06007_M09_octanol_pH-metric high logP_report.pdf
+SM11,2.09,0.01,pH-metric octanol logP,M11,18B-27016,c1ccc(cc1)n2c3c(cn2)c(ncn3)N,SM11_18B-27016_M11_octanol_pH-metric high logP_report.pdf
+SM11,2.19,0.02,pH-metric octanol logP,M11,18C-01001,c1ccc(cc1)n2c3c(cn2)c(ncn3)N,SM11_18C-01001_M11_octanol_pH-metric high logP_report.pdf
+SM11,2.01,0.02,pH-metric octanol logP,M11,18C-01002,c1ccc(cc1)n2c3c(cn2)c(ncn3)N,SM11_18C-01002_M11_octanol_pH-metric high logP_report.pdf
+SM11,2.12,0.01,pH-metric octanol logP,M11,18C-09010,c1ccc(cc1)n2c3c(cn2)c(ncn3)N,SM11_18C-09010_M11_octanol_pH-metric high logP_report.pdf
+SM12,3.79,0.02,pH-metric octanol logP,M12,18C-01012,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)Cl.Cl,SM12_18C-01012_M12_octanol_pH-metric high logP_report.pdf
+SM12,3.81,0.01,pH-metric octanol logP,M12,18C-03013,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)Cl.Cl,SM12_18C-03013_M12_octanol_pH-metric high logP_report.pdf
+SM12,3.91,0.01,pH-metric octanol logP,M12,18C-03014,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)Cl.Cl,SM12_18C-03014_M12_octanol_pH-metric high logP_report.pdf
+SM12,3.80,0.01,pH-metric octanol logP,M12,18C-03015,c1ccc2c(c1)c(ncn2)Nc3cccc(c3)Cl.Cl,SM12_18C-03015_M12_octanol_pH-metric high logP_report.pdf
+SM13,2.87,0.01,pH-metric octanol logP (predose 100 uL octanol),M13,18C-09011,Cc1cccc(c1)Nc2c3cc(c(cc3ncn2)OC)OC,SM13_18C-09011_M13_octanol_pH-metric high logP_report.pdf
+SM13,2.89,0.02,pH-metric octanol logP (predose 100 uL octanol),M13,18C-16016,Cc1cccc(c1)Nc2c3cc(c(cc3ncn2)OC)OC,SM13_18C-16016_M13_octanol_pH-metric high logP_report.pdf
+SM13,2.99,0.03,pH-metric octanol logP (predose 200 uL octanol),M13,18C-26010,Cc1cccc(c1)Nc2c3cc(c(cc3ncn2)OC)OC,SM13_18C-26010_M13_octanol_pH-metric high logP_report.pdf
+SM14,1.92,0.01,pH-metric octanol logP,M15,18B-28002,c1ccc(cc1)n2cnc3c2ccc(c3)N,SM14_18B-28002_M15_octanol_pH-metric high logP_report.pdf
+SM14,1.92,0.01,pH-metric octanol logP,M15,18C-01004,c1ccc(cc1)n2cnc3c2ccc(c3)N,SM14_18C-01004_M15_octanol_pH-metric high logP_report.pdf
+SM14,1.93,0.01,pH-metric octanol logP,M15,18C-01005,c1ccc(cc1)n2cnc3c2ccc(c3)N,SM14_18C-01005_M15_octanol_pH-metric high logP_report.pdf
+SM14,2.04,0.02,pH-metric octanol logP,M15,18C-03006,c1ccc(cc1)n2cnc3c2ccc(c3)N,SM14_18C-03006_M15_octanol_pH-metric high logP_report.pdf
+SM15,3.14,0.01,pH-metric octanol logP,M16,18C-01007,c1ccc2c(c1)ncn2c3ccc(cc3)O,SM15_18C-01007_M16_octanol_pH-metric high logP_report.pdf
+SM15,3.04,NaN,pH-metric octanol logP,M16,18C-01008,c1ccc2c(c1)ncn2c3ccc(cc3)O,SM15_18C-01008_M16_octanol_pH-metric high logP_report.pdf
+SM15,3.04,0.01,pH-metric octanol logP,M16,18C-01009,c1ccc2c(c1)ncn2c3ccc(cc3)O,SM15_18C-01009_M16_octanol_pH-metric high logP_report.pdf
+SM16,2.63,0.01,pH-metric octanol logP (predose 100 uL octanol),M18,18C-09014,c1cc(c(c(c1)Cl)C(=O)Nc2ccncc2)Cl,SM16_18C-09014_M18_octanol_pH-metric high logP_report.pdf
+SM16,2.59,0.01,pH-metric octanol logP (predose 100 uL octanol),M18,18C-09015,c1cc(c(c(c1)Cl)C(=O)Nc2ccncc2)Cl,SM16_18C-09015_M18_octanol_pH-metric high logP_report.pdf
+SM16,2.63,0.02,pH-metric octanol logP (predose 100 uL octanol),M18,18C-09016,c1cc(c(c(c1)Cl)C(=O)Nc2ccncc2)Cl,SM16_18C-09016_M18_octanol_pH-metric high logP_report.pdf
diff --git a/physical_properties/logP/experimental_data/mean_and_SEM_calculation.png b/physical_properties/logP/experimental_data/mean_and_SEM_calculation.png
diff --git a/physical_properties/pKa/experimental_data/README.md b/physical_properties/pKa/experimental_data/README.md
@@ -6,6 +6,9 @@ Please see [SAMPL6/pKa Challenge Instructions/Experimental Details](https://gith
 `pKa_experimental_values.csv` file contains mean and standard error of the mean(SEM) of experimental macroscopic pKa values, calculated using `calc_pKa_value_statistics.py` script.
 Since pKa values measured by Sirius T3 were reported with 2 decimal places, we have reported SEM as 0.01 in cases where SEM values calculated from 3 replicates were lower than 0.01.  
 
+### Publication on pKa measurements
+Mehtap Işık, Dorothy Levorse, Ariën S. Rustenburg, Ikenna E. Ndukwe, Heather Wang, Xiao Wang, Mikhail Reibarkh, Gary E. Martin, Alexey A. Makarov, David L. Mobley, Timothy Rhodes, John D. Chodera. "pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments" _J Comput Aided Mol Des_ (2018) 32: 1117. https://doi.org/10.1007/s10822-018-0168-0
+
 ## Manifest
 - `pKa_experimental_values.csv` - Mean and SEM of pKa values organized in a table. Up to three pKa values were reported based on how many pKas were measured in the experimental interval of 2-12.
 - `calc_pKa_value_statistics.py` - Python script used to calculate mean and SEM of pKa values from `pKa_results_of_replicate_experiments.csv`.