issues
search
openforcefield
/
protein-ligand-benchmark
Protein-Ligand Benchmark Dataset for Free Energy Calculations
MIT License
144
stars
15
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Missing ligands in .yaml files for HIF2A and MCL1
#111
rgorantla04
opened
1 month ago
0
Clean up `ligands.yaml` files
#110
IAlibay
opened
2 months ago
1
New tag/release?
#109
mattwthompson
closed
2 months ago
2
Docs -- examples on running benchmarks with alchemiscale
#108
ijpulidos
opened
7 months ago
1
Error when trying to assign partial charges to the eg5 cofactor using openff-toolkit/openeye am1bccelf10
#107
hannahbaumann
opened
7 months ago
1
Changes PLB from openfe
#106
hannahbaumann
closed
2 months ago
13
Use OpenEye tools for pose generation/preparation?
#105
ijpulidos
opened
10 months ago
0
Ring substituents for some ligands in different orientations, even though same substituent
#104
hannahbaumann
opened
11 months ago
1
[WIP] Changes to PLB
#103
hannahbaumann
closed
11 months ago
0
Include data from latest Schrodinger's public dataset
#102
ijpulidos
opened
11 months ago
0
Questions regarding specific ligands in the PLB
#101
hannahbaumann
opened
11 months ago
4
lomap networks
#100
hannahbaumann
opened
1 year ago
1
Lomap networks [ WIP don't merge ]
#99
hannahbaumann
closed
1 year ago
0
Manually curated edges by Ken Takaba
#98
ijpulidos
closed
1 year ago
4
Check stability of ligand poses in long MD simulations
#97
jchodera
opened
1 year ago
0
Add manually curated transformation network
#96
ijpulidos
opened
1 year ago
0
Adding star maps yaml files
#95
hannahbaumann
closed
1 year ago
0
doi listed for eg5 ligand data is incorrect
#94
dkozuch
opened
1 year ago
0
[WIP] Adding network edges
#93
IAlibay
opened
1 year ago
6
structure of edges yamls
#92
richardjgowers
opened
1 year ago
2
cMET only has 5 cmpds now
#91
bcossins
opened
1 year ago
2
Update of README.md Summary needed
#90
mvkrier
opened
1 year ago
2
For CI, add PDB reading and FF application via OpenMM, ambertools (leap template) for all targets
#89
dotsdl
opened
1 year ago
0
Connectivity for NME caps is missing
#88
IAlibay
closed
1 year ago
1
Various PDB fixes
#87
IAlibay
closed
1 year ago
5
YAML Schema
#86
mikemhenry
opened
1 year ago
1
Remove `.maegz` files from `main` history, if possible
#85
dotsdl
opened
1 year ago
0
Thrombin PDB unusual residue indexes
#84
JSLJ23
closed
1 year ago
3
Adding new directory structure for edges
#83
IAlibay
closed
1 year ago
14
Addressing issues 75 & 81
#82
bobym
closed
1 year ago
13
Abnormal ligand conformations
#81
IAlibay
closed
1 year ago
0
SHP2 ligands have some suspect conformations
#80
Yoshanuikabundi
opened
2 years ago
2
Choice of ligands in the repo
#79
annamherz
opened
2 years ago
2
[WIP] Restructuring repo around 'data'; moved 'data' into python package
#78
dotsdl
opened
2 years ago
0
Restructure repo with `data` included within Python package
#77
dotsdl
opened
2 years ago
0
[WIP] Fix MCL1 capping, curate thrombin ligands for expanded dynamic range
#76
bobym
closed
1 year ago
1
MCL-1 is not capped at C terminus?
#75
IAlibay
closed
1 year ago
3
Remove `cd2_ligs` directory and zip file in `cdk2`?
#74
IAlibay
opened
2 years ago
0
Investigate clashes
#73
IAlibay
opened
2 years ago
2
Investigate abnormal ligand conformations in CDK8
#72
IAlibay
closed
1 year ago
1
Presence of two PDBs for Thrombin
#71
IAlibay
opened
2 years ago
2
Update (or remove?) `targets.yaml` data file
#70
ijpulidos
opened
2 years ago
2
Remove old edges.yaml files, replace with new calculated ones
#69
IAlibay
closed
1 year ago
0
Fix PDB files
#68
IAlibay
closed
1 year ago
1
Fix Python API, CI, and remove "example" files
#67
IAlibay
opened
2 years ago
0
Document changes to the PLB set
#66
IAlibay
opened
2 years ago
0
Generate benchmark data
#65
IAlibay
opened
2 years ago
1
Protonation state of HIS248 in HIF2A needs to be adapted
#64
Gilli08
opened
2 years ago
1
Inconsistencies between preparation and assay conditions
#63
IAlibay
opened
2 years ago
0
Redesign Science re-curated benchmark
#62
jchodera
opened
2 years ago
1
Next