Version 1.1: Update logP analysis; release PHIP2 analysis

This release includes these additional updates:

• 2021-10-05: Update two logP/logD experimental values (SM41 and SM43) to reflect an error in the experimental values provided us, as discussed in a forthcoming erratum to the experimental study from the Ballatore lab.
• 2021-10-20: Update with details to Ballatore lab corrigendum
• 2021-10-26: Add PHIP2 protein-ligand analysis.

Correct two submissions, update analysis, and finalize logD analysis

This point release:

• Fixed two log P submissions that had errors and updated the overview plots/stats and individual plots for the two affected submissions (4/9/2021)
• Finalizes logD analysis, after fixing the two log P submissions that had errors (regenerating estimates/doing plots) (4/19/2021)

Version 0.8: Add initial logD notebook

Adds initial logD notebook/analysis from Tielker. This is a retroactive release to tag specific older commits.

Version 0.7: Add physical property analysis

Add physical properties analysis for logP and pKa. This is a retroactive point release to tag specific older commits.

Version 0.6: Add logP challenge inputs/experimental results

This release includes changes previously pushed to master; essentially, it finalizes the physical properties challenge inputs, formats, submissions and experimental results. A later release will include the results of analysis.

Detailed changelog since 0.5.0 release:

• Finalize physical property format (Sept. 1, 2020): Update submission formats to include some required fields that had previously been left out (e.g. participant name/organization, and whether submission is ranked). Changed required format for logP and permeability to better handle molecule ID/choice of tautomer.
• Add SAMPL7 physical property submission links (Sept. 2, 2020)
• Update physical property submission deadline to Oct. 8 (Sept. 28, 2020).
• Update physical property instructions for pKa, logP to clarify (Sept. 30, 2020). Format still the same, but now clarified -- especially for the pKa challenge. We also now highly encourage submission of (optional) logD predictions for the logP challenge.
• Added additional microstates for pKa challenge, from Bogdan Iorga (Sept. 30, 2020). Updated instructions to clarify that any states not included in pKa predictions will be assumed to be unpopulated (so participants can omit these states). Updated pKa instructions/template to allow optional submission of macro pKa values.
• Note that experiments used specified chirality for certain physical property compounds, SM35, SM36 and SM37. So only the structures with specified chirality for these compounds should be used.
• Add SAMPL7 physical properties experimental values (Oct. 10, 2020).
• Add SAMPL7 physical properties submissions (Oct. 10, 2020)

Version 0.5: Add PHIP2, physical property challenge

This version incorporates diverse changes since the last release, particularly incorporation of the PHIP2 protein-ligand challenge data, and release of the physical property challenge details. These changes include:

• (12/2/2019): Add PHIP2 Stage 2 inputs
• (12/5/2019): Add PHIP2 Stage 2 submission format. Submission link still to come.
• (12/7/2019): Add PHIP2 example submission package.
• (12/7/2019): Add link to bare-bones PHIP2 Stage 2 submission uploads -- open for submissions.
• (12/11/2019): Update PHIP2 stage 2 deadline to noon US Pacific time Dec. 14.
• (12/12/2019): Correct a single exoOA value (for G2) binding, per e-mail from Bruce Gibb.
• (2019-12-14): Add crystal structures of PHIP2 hits, instructions for stage 3.
• (2019-12-20): Add Isaacs' TrimerTrip reference. Add Zenodo DOI for modified cyclodextrin raw experimental data.
• (2019-12-20): Add Stage 2 submissions for PHIP2.
• (2019-12-23): Add Stage 3 submission format for PHIP2.
• (2019-12-23): Add preliminary host-guest analysis (ranked submissions only, for now) for GDCC and TrimerTrip; add preliminary first pass at CD analysis.
• (2020-01-08): Add PHIP2 Stage 3 submission upload.
• (2020-01-14): Include informal reference calculations for trimertrip, GDCC, CD.
• (2020-01-17): Add PHIP2 Stage 3 submissions.
• (2020-02-14): Add additional host-guest analysis/updates to analysis. Include reference calculations in analysis, clean up files.
• (2020-04-10): Add link to host-guest virtual workshop program/video
• (2020-06-29): Add preliminary details of the SAMPL7 physical property challenge on pK_a, log P, and permeability.
• (2020-07-07): Compounds renumbered for the SAMPL7 physical property challenge on pKa, log P, and permeability.
• (2020-08-06): Add physical property submission formats, templates

Add host-guest data, correct some SMILES

This release incorporates various changes made to master previously, including:

• (11/2/19, PHIP2) Fix misformatted SMILES line on line 620 of fragments_screened.csv for PHIP2 screening challenge.
• (11/11/19, PHIP2) Fix an incorrect SMILES for fragment F62 in the PHIP2 screening challenge.
• (11/12/19, PHIP2) Add participation instructions and submission format for PHIP2 virtual screening component (Stage 1).
• (11/15/19, host-guest) Add TrimerTrip and cyclodextrin experimental binding data (first draft). Update Gibb data with additional precision/correct rounding errors.
• (11/18/19, host-guest) Fix typo in one of values, for MGLab_36-g2
• (11/25/19, protein-ligand): Add submission link for protein-ligand virtual screening challenge at http://sampl-submission.us-west-1.elasticbeanstalk.com/submit
• (11/27/19, protein-ligand): Clarify some aspects of instructions and submission deadline.

The largest changes are that:

1. Host-guest experimental values are now provided
2. The protein-ligand Stage 1 challenge submission information and SMILES are available/correct (though the SMILES were available at an earlier date, this release formalizes them).

Version 0.4: Protein-ligand challenge addition, add TrimerTrip data

Adds Isaacs' group TrimerTrip binding data (in host_guest/analysis/ExperimentalMeasurements); adds TrimerTrip submissions; adds PHIP2 protein-ligand challenge Stage 1 details.

Version 0.3: Improve charge states and residue names for CDs

This fixes some issues with listed formal charges for modified cyclodextrin hosts (some of these issues were corrected earlier, but the table listing likely formal charges was still incorrect) and also fixes a problem with the NAME of a carbon atom in some of the cyclodextrin hosts which was causing problems for some modified cyclodextrin hosts (it was named 'HQ' in some cases). See #42 for full details.

This also make several other improvements to modified cyclodextrins (improving images, improving PDB CONECT entries etc.).

Additionally this clarifies several issues in README.md files and descriptions of submission formats.

Version 0.2: Submission details

Adds host-guest submission template files and instructions; makes more clear which compounds/cases are optional; makes clear that free energy predictions (and uncertainties) are required; enthalpies optional; adds links to host-guest submission system