Merge pull request #124 from samplchallenges/pka-analysis

pKa analysis

physical_property/README.md

@@ -2,7 +2,7 @@
 We are excited to announce a new set of SAMPL7 challenges focusing on pK<sub>a</sub>, partitioning, and permeability. [The Ballatore group at UCSD](https://pharmacy.ucsd.edu/faculty/ballatore) is contributing a set of measured water-octanol log *P*, log *D*, and pK<sub>a</sub> values for 22 compounds. They also provided Parallel Artificial Membrane Permeability Assay (PAMPA) permeability and melting point values they measured.
 
 
-pK<sub>a</sub> prediction will consist of predicting relative free energies between compound microstates (which could be also thought of as the reaction free energy for that particular microstate transition; [see pKa instructions](https://github.com/samplchallenges/SAMPL7/blob/master/physical_property/pKa/pKa_challenge_instructions.md)). We choose free energies rather than pK<sub>a</sub> values given the recent work of [Gunner et al.](https://link.springer.com/content/pdf/10.1007/s10822-020-00280-7.pdf). For the purposes of the pK<sub>a</sub> challenge all possible tautomers of each ionization (charge) state are defined as distinct protonation microstates. Macro pK<sub>a</sub> values may be submitted to allow for a consistency check.
+pK<sub>a</sub> prediction will consist of predicting relative free energies between compound microstates (which could be also thought of as the reaction free energy for that particular microstate transition; [see pK<sub>a</sub> instructions](https://github.com/samplchallenges/SAMPL7/blob/master/physical_property/pKa/pKa_challenge_instructions.md)). We choose free energies rather than pK<sub>a</sub> values given the recent work of [Gunner et al.](https://link.springer.com/content/pdf/10.1007/s10822-020-00280-7.pdf). For the purposes of the pK<sub>a</sub> challenge all possible tautomers of each ionization (charge) state are defined as distinct protonation microstates. Macro pK<sub>a</sub> values may be submitted to allow for a consistency check.
 
 The partitioning prediction challenge will focus on predicting the difference in free energy for the neutral form between water and octanol. As a part of post prediction analysis challenge oraginzers will combine participant-predicted pK<sub>a</sub> and log *P* values to obtain estimated distribution coefficients, which will also be compared against experimental values. Participants may optionally submit their own log *D* values for a consistency check.
 
@@ -19,7 +19,7 @@ Submissions to the SAMPL7 physical property challenge will be due October 8, 202
 
 Submission details, templates, instructions and analysis are linked to in the manifest.
 
-The submission servers are now live: [SAMPL7 pKa submissions](http://sampl-submit.us-west-1.elasticbeanstalk.com/submit/SAMPL7-pKa) and [SAMPL7 logP/permeability submissions](http://sampl-submit.us-west-1.elasticbeanstalk.com/submit/SAMPL7-physprop)). Note that each challenge component has its own format, but logP and permeability share the same submission URL.
+The submission servers are now live: [SAMPL7 pK<sub>a</sub> submissions](http://sampl-submit.us-west-1.elasticbeanstalk.com/submit/SAMPL7-pKa) and [SAMPL7 logP/permeability submissions](http://sampl-submit.us-west-1.elasticbeanstalk.com/submit/SAMPL7-physprop). Note that each challenge component has its own format, but logP and permeability share the same submission URL.
 
 ## A view of the compounds
 
@@ -40,8 +40,8 @@ Effective permeability (log<sub>*P*<sub>*app*</sub></sub>) was measured by PAMPA
 ## What's here
 
 - [`SAMPL7_molecule_ID_and_SMILES.csv`](SAMPL7_molecule_ID_and_SMILES.csv): A `.CSV` file containing SAMPL7 challenge molecule IDs and SMILES. SMILES were provided by the [Ballatore lab](https://pharmacy.ucsd.edu/faculty/ballatore).
-- [`logP/`](logP/): Folder contains an input file in `.CSV` format with SMILES strings of the neutral states of the molecules. This folder contains participant submissions, instructions, a submission template and the analysis for the logP challenge.
-- [`pKa/`](pKa/): Folder contains challenge input files in `.CSV` format with SMILES of enumerated microstates. `.MOL2` and `.SDF` files of each microstate are also provided. This folder contains instructions and a submission template for the pKa challenge. This folder will be updated to contain analysis. Microstates (tautomers and protomers) were generated with a notebook wich uses RDKit and OpenEye tools. Additional microstates were enumerated using Chemicalize (Chemaxon) and Epik (Schrodinger) and added to the notebook generated `.CSV` files.
+- [`logP/`](logP/): This folder contains participant submissions, instructions, a submission template and the analysis for the log *P* challenge. Also contains an input file in `.CSV` format with SMILES strings of the neutral states of the molecules.
+- [`pKa`](pKa/): This folder contains instructions, a submission template and the analysis for the pK<sub>a</sub> challenge. Also contains challenge input files in `.CSV` format with SMILES of enumerated microstates and both `.MOL2` and `.SDF` files of each microstate. This folder contains instructions and a submission template for the pK<sub>a</sub> challenge. Microstates (tautomers and protomers) were generated with a notebook wich uses RDKit and OpenEye tools. Additional microstates were enumerated using Chemicalize (Chemaxon) and Epik (Schrodinger) and added to the notebook generated `.CSV` files.
 - [`permeability/`](permeability/): Folder contains input files in `.CSV` format with SMILES strings of molecules. This folder contains instructions, a submission template and the analysis for the permeability challenge.
 - [`images/`](images): Folder containing images related to this challenge in PDF and/or JPEG format.
 - [`experimental_data/`](experimental_data/): Folder contains experimental measurements of pK<sub>a</sub>, partitioning, and permeability values.

physical_property/pKa/README.md

@@ -16,4 +16,4 @@ Experimental pK<sub>a</sub> measurements will made available after the challenge
 - [`example_submission_file/pKa-DanielleBergazinExampleFile-1.csv`](example_submission_file/pKa-DanielleBergazinExampleFile-1.csv) - An example submission file filled with random values to illustrate expected format.
 - [`pKa_challenge_instructions.md`](pKa_challenge_instructions.md) - Instructions for the pK<sub>a</sub> challenge.
 - [`transition_networks/`](transition_networks/) - This directory contains transition networks of the challenge molecules in `.PDF` and `.PPTX` format.
-- `Analysis`: Contains submissions, and will eventually contain results of analysis.
+- [`analysis`](analysis/): Contains participant submissions and analysis results.

physical_property/pKa/analysis/README.md

@@ -0,0 +1,5 @@
+## Manifest
+
+- [`macrostate_analysis/`](macrostate_analysis/) - This directory contains analysis outputs of pK<sub>a</sub> predictions. See the more detailed [README](macrostate_analysis/README.md) for details.
+- [`microstate_analysis/`](microstate_analysis/) - This directory contains analysis outputs of relative microstate free energy submissions. See the more detailed [README](microstate_analysis/README.md) for details.
+- [`relative_microstate_free_energy_predictions/`](relative_microstate_free_energy_predictions/) - Contains participant relative microstate free energy submissions. Contains a folder which holds original submissions, some of which had errors and needed to be updated after the challenge deadline. Submissions had their submitted names changed to be more descriptive in analysis graphs.