MobleyLab benchmarksets issues

MobleyLab / benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards

BSD 3-Clause "New" or "Revised" License

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issues

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fix bonds and protonation for BRD4 ligand 5

#74 GHeinzelmann opened 3 years ago
2
gdcc-set2 and CB experimental Delta H is missing

#73 saharctech closed 3 years ago
4
Include additional data, references

#72 davidlmobley opened 4 years ago
0
Fix BRD4 solvated complex PDB files to include `CONECT` records

#71 jchodera closed 4 years ago
1
PDB files for BRD4 parameterized systems are missing CONECT records

#70 jchodera closed 4 years ago
2
Fix SDF files

#69 guoweiqi closed 4 years ago
1
The SDF files for charged compounds aren't listing the formal charges of the atoms

#68 guoweiqi opened 5 years ago
2
Add machine-readable tables for all the sets

#67 slochower opened 6 years ago
3
[WIP] T4 Lysozyme input files

#66 andrrizzi opened 6 years ago
9
Resolve issue 63.

#65 davidlmobley closed 6 years ago
0
Errors using cyclic host `mol2` files with non-unique atom names

#64 slochower closed 6 years ago
11
Typo in reference for Lysozyme L99A/M102Q - catechol experimental value?

#63 andrrizzi closed 6 years ago
3
Mixed 1-4 scaling?

#62 davidlmobley opened 7 years ago
2
Update README.md to reflect how to cite (once discussion is final)

#61 ghost closed 7 years ago
4
Parmed bug affecting cyclodextrin files

#60 andrrizzi opened 7 years ago
6
Jiyin

#59 ghost closed 6 years ago
2
Update version number for ongoing development

#58 davidlmobley closed 7 years ago
0
Update for version 1.3 release

#57 davidlmobley closed 7 years ago
0
Update README.md to reflect BRD4(1) changes

#56 davidlmobley closed 7 years ago
3
Provide compound ID for all files

#55 davidlmobley opened 7 years ago
5
Should we use table titles and not numbers in markdown files?

#54 davidlmobley opened 7 years ago
6
Deposit calculated values for provided files when available

#53 davidlmobley opened 7 years ago
5
This is a PR which condenses a single paragraph

#52 davidlmobley closed 7 years ago
3
Incorporate minor edits of new cyclodextrin material into nieldev branch

#51 davidlmobley closed 7 years ago
0
Provide bound-state starting structures for hosts

#50 davidlmobley opened 7 years ago
5
Provide suitable README files for CB7, GDCC benchmarks

#49 davidlmobley opened 7 years ago
0
Update/reorganize input files for BRD4(1); rename ligands in tables for consistency with rest of table

#48 GHeinzelmann closed 7 years ago
16
Add CD benchmarks to manuscript

#47 nhenriksen closed 7 years ago
35
Bump version/update README

#46 davidlmobley closed 7 years ago
0
Get CD benchmarks in?

#45 davidlmobley closed 7 years ago
3
CD mol2/pdb/sd files coordinates starting in the binding pocket

#44 andrrizzi closed 7 years ago
3
Prep v1.1.4 release

#43 davidlmobley closed 7 years ago
0
Add additional supplementary data, perhaps in markdown files?

#42 davidlmobley opened 7 years ago
5
CD mol2 files coordinates starting in the binding pocket

#41 andrrizzi opened 7 years ago
20
Edit Germano PR

#40 davidlmobley closed 7 years ago
0
Mobley heinzelmann

#39 GHeinzelmann closed 7 years ago
0
Edits/comments

#38 davidlmobley closed 7 years ago
0
Tweaks to README.md and paper to clarify AR relationship

#37 davidlmobley closed 7 years ago
0
Add info on bromodomain benchmark

#36 GHeinzelmann closed 7 years ago
22
bioRxiv won't take preprints, so migrate to eScholarship

#35 davidlmobley closed 7 years ago
0
Update README.md to link to AR published version

#34 davidlmobley closed 7 years ago
0
Update for ongoing development

#33 davidlmobley closed 7 years ago
0
Update for version 1.1.3

#32 davidlmobley closed 7 years ago
0
update license to BSD-3

#31 davidlmobley closed 7 years ago
0
Update for ongoing development; add Zenodo DOI.

#30 davidlmobley closed 7 years ago
0
Cleanup README.md, add AR acknowledgments, bromodomain reference

#29 davidlmobley closed 7 years ago
0
Update to reflect new release

#28 davidlmobley closed 7 years ago
0
Update to include revisions made for AR; minor other adjustments

#27 davidlmobley closed 7 years ago
0
Minor edits to improve figure captions

#26 davidlmobley closed 7 years ago
3
Update README.md to reflect new input files

#25 davidlmobley closed 7 years ago
0