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Releases: MobleyLab/benchmarksets

Version 1.3

28 Aug 17:16
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  • Includes cyclodextrin benchmarks to data and to paper
  • Removes of most of cyclodextrin material from future benchmarks since it is now included in main body
  • Addition of Niel Henriksen as an author based on his work on the cyclodextrin component
  • BRD4(1) changes: Reorganize data files; improve BRD4(1) README; switch sd to sdf files; give each BRD4(1) ligand a unique identifier specific to this paper.

Version 1.2

04 Aug 20:19
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  • Incorporates new proposed bromodomain (BRD4(1)) benchmark set on ligands studied partly by Matteo Aldeghi, Phil Biggin, and Germano Heinzelmann
  • Adds Heinzelmann as an author
  • Adds bromodomain input files

Version 1.1.4

03 Aug 00:24
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  • Updates README.md to reflect publication; clarify differences in material; reflect availability on eScholarship.
  • Updates paper to reflect migration to eScholarship rather than bioRxiv.

Version 1.1.3

03 May 20:48
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This version:

  • Updates the README.md to make clear how to access the always-up-to-date version of this paper
  • Amends the title of the paper to indicate that this is the perpetual review version

Version 1.1.2

27 Apr 19:56
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This version:

  • Fixes some minor grammar issues
  • Adds consistently handled SMILES for aromatics
  • Adds Annual Reviews copyright/rights info in TeX and README
  • Adds additional citation information for one reference
  • Adds new discussion of some new bromodomain absolute binding free energy work

Version 1.1.1

20 Jan 23:50
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This version:

  • adds host-guest input files
  • updates some figure captions
  • makes various edits recommended by Annual Reviews to that version of the paper (which is now separate from this one, but there is still some overlap) including some clarification of scope, more discussion of SAMPL and D3R, and more discussion of why lysozyme was chosen and what complexities there are in the system

Version 1.1

08 Dec 23:26
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This release makes a number of significant changes:

  • Incorporates material on potential future benchmark systems which we had cut for space reasons for journal submission, including a fairly extensive section on cyclodextrins
  • Adds a discussion on the need for workflow science to help advance our methods and assess them
  • Inserts a small amount of additional discussion elsewhere which had been cut for space reasons
  • Adds a version number, date, and link back to this repo on the first page of the paper|
  • Fixes some incomplete references

Version 1.0.4

17 Nov 20:12
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Same as version 1.0.2 but includes correct PDF file.

Version 1.0.2

17 Nov 20:07
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Add an additional reference relating to domain of applicability, link to some host-guest data newly posted in BindingDB, and fix an error in a PDB code. Some other minor maintenance done which does not affect the content.

Incorporates #18 and is a maintenance release preceding more substantial modifications.

Version 1.0.1

26 Sep 16:24
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Version 1.0.1 -- incorporates typo fixes and improved tables from David Slochower. Not necessarily enough different from the original that it merits a new release, but I want to get a Zenodo DOI in for this, and this release will trigger that.