Merge pull request #54 from samplchallenges/PHIP2

Update README files for 0.4 release

README.md

@@ -6,7 +6,7 @@ Challenge details, inputs, and (eventually) results for the SAMPL7 series of cha
 
 See the [SAMPL website](https://samplchallenges.github.io) for information on the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) series of challenges as a whole. This repository focuses specifically on the SAMPL7 series of challenges.
 
-Because these files are available publicly, we have no record of who downloads them. Therefore, you should sign up for notifications. Specifically, if you want to receive updates if we uncover any problems, it is imperative that you either (a) sign up for the SAMPL e-mail list via the D3R site, or (b) sign up for notifications of changes to this GitHub repository (the Watch button, above); ideally you would do both.
+Because these files are available publicly, we have no record of who downloads them. Therefore, you should sign up for notifications. Specifically, if you want to receive updates if we uncover any problems, it is imperative that you either (a) sign up for the SAMPL e-mail list, or (b) sign up for notifications of changes to this GitHub repository (the Watch button, above); ideally you would do both.
 Join our [SAMPL7 e-mail list](http://eepurl.com/gpBBun) to get e-mails with SAMPL7-related announcements.
 
 ## What's here
@@ -18,7 +18,7 @@ Join our [SAMPL7 e-mail list](http://eepurl.com/gpBBun) to get e-mails with SAMP
 - [Host-guest participation instructions](host_guest_instructions.md) with information on the submission format, etc. Our submission system is also [now available](http://sampl-submission.us-west-1.elasticbeanstalk.com/submit/). Submission formats are available in the subdirectories for the individual host-guest systems.
 - Protein-ligand details on the [PHIP2 challenge](protein_ligand/README.md), in the `protein_ligand` directory.
 
-All three host-guest components of this challenge are now final and launched, though additional supporting files may be added at a later date. **The submission deadline is Oct. 4 for the TrimerTrip host-guest challenge and Nov. 1 for the cyclodextrin derivatives and GDCC challenges**, due to timescales for data collection and publication of the experimental data. The first stage of the protein-ligand challenge is due Nov. 28, 2019.
+All three host-guest components of this challenge are now final and launched, though additional supporting files may be added at a later date. **The submission deadline is Oct. 4 for the TrimerTrip host-guest challenge and Nov. 1 for the cyclodextrin derivatives and GDCC challenges**, due to timescales for data collection and publication of the experimental data. The **first stage of the protein-ligand challenge is due Nov. 28, 2019.**
 
 ## What's coming
 - GSK logD challenge information as soon as available
@@ -30,7 +30,7 @@ All three host-guest components of this challenge are now final and launched, th
 ## Disclaimers:
 - As usual, we make no warranty as to correctness of protonation states, tautomers, conformations and poses provided in these directories. In some cases the most relevant such states may not be known, or multiple states perhaps should be considered. Please exercise caution and due diligence.
 - We make an effort to indicate which files are original source files, and which are derived files, so that participants can refer to the original source files to help resolve any uncertainties. We encourage participants to do so.
-- While we make every effort to ensure correctness of the files we provide, it is not uncommon for there to be some errors. *Please* sign up for our e-mail list, since if any critical bugs are found, we will e-mail out appropriate announcements.
+- While we make every effort to ensure correctness of the files we provide, it is not uncommon for there to be some errors. **Please sign up for our [e-mail list](http://eepurl.com/gpBBun)**, since if any critical bugs are found, we will e-mail out appropriate announcements.
 
 ## Changes and Data Set Versions
 
@@ -40,14 +40,9 @@ All three host-guest components of this challenge are now final and launched, th
 - **Release 0.1.2** (Sept. 16, 2019, DOI [10.5281/zenodo.3432298](https://dx.doi.org/10.5281/zenodo.3432298)): Fixes protonation states for three "modified cyclodextrin" hosts which had accidentally been prepared (and drawn in ChemDraw) with charged groups present as neutral -- specifically terminal -NH3 groups were provided as -NH2. This affected MGLab19, 24 and 34. Also includes minor maintenance fixes -- listing final rather than tentative buffer conditions for GDCC case (just removing the "tentative" on the buffer identity, and correcting pH from 11.5 to 11.7); updates submission deadlines; fixes missing coordinates in TrimerTrip `g11`; fixing breakdown into residues in a couple modified cyclodextrin host PDB/mol2 files.
 - **Release 0.2** (Sept. 24, 2019, DOI [10.5281/zenodo.3459975](https://dx.doi.org/10.5281/zenodo.3459975)): 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](http://sampl-submission.us-west-1.elasticbeanstalk.com/submit/)
 - **Release 0.3** (Sept. 26, 2019, DOI [10.5281/zenodo.3462865](https://dx.doi.org/10.5281/zenodo.3462865)): Corrected likely charges/protonation states for MGLab23 and MGLab24 in overview table and in jpg and PDF files. Updated corresponding coded and noncoded CDX files. Fixed a mixture of UNK and MGO residue names. Eliminates all instances of atom name HQ which should correspond to a carbon (which for some reason was instead named HX in some hosts, likely causing problems for some workflows). This has been mapped to atom name C9. Reconnects missing bonds in the PDB section of several models. See [PR 42](https://github.com/MobleyLab/SAMPL7/pull/42) for full details. Also removes outdated info in README.md and removes extra guest listed in TrimerTrip submission template.
+- **Release 0.4** (Oct. 30, 2019)): Adds Isaacs' group TrimerTrip binding data (in `host_guest/analysis/ExperimentalMeasurements`); adds TrimerTrip submissions; adds PHIP2 protein-ligand challenge Stage 1 details.
 
 ### Changes not in a release
-- Update TrimerTrip deadline to Oct. 4.
-- Add Isaacs' group TrimerTrip binding data 10/14/19 (in `host_guest/analysis/ExperimentalMeasurements`)
-- Update Isaacs' group TrimerTrip binding data to give n value from fit
-- Add TrimerTrip submissions.
-- Add preliminary info on bromodomain fragment binding challenges (10/25/19)
-- Add PHIP2 protein-ligand challenge Stage 1 details (10/29/2019)
 
 ## Challenge overview
 
@@ -65,7 +60,7 @@ This challenge breaks out into at least three stages on a tight timeline:
 2) Prediction of fragment binding modes
 3) Selection of new compounds for screening from an experimental database
 
-Stage 1 is now open and focuses on identification of binders. Unfortunately, the timeline for stages 1 and 2 has to be tight given the timeframe for experimental compound screening (Stage 3).
+Stage 1 is now open and focuses on identification of binders. Unfortunately, the timeline for stages 1 and 2 has to be tight given the timeframe for experimental compound screening (Stage 3). See [protein_ligand/README.md](protein_ligand/README.md) for full details.
 
 
 ### Gibb Deep Cavity Cavitand (GDCC) binding of guests

protein_ligand/README.md

@@ -12,7 +12,7 @@ This challenge breaks out into at least three phases on a tight timeline:
 
 Phase 1 is now open and focuses on identification of binders. Unfortunately, the timeline for components 1 and 2 has to be tight given the timeframe for experimental compound screening (Phase 3).
 
-If you plan to participate, please [join our SAMPL7 e-mail list](https://drugdesigndata.us19.list-manage.com/subscribe?u=8181f49f8d2daca876bc86225&id=44c32db76e) so we can keep you updated.
+If you plan to participate, please [join our SAMPL7 e-mail list](http://eepurl.com/gpBBun) so we can keep you updated.
 
 ## System background