openforcefield/protein-ligand-benchmark

Issues

• Clean up `ligands.yaml` files

  #110 opened 2 months ago by IAlibay
  1

• Choice of ligands in the repo

  #79 opened 2 years ago by annamherz
  2

• New tag/release?

  #109 opened 2 months ago by mattwthompson
  2

• Docs -- examples on running benchmarks with alchemiscale

  #108 opened 6 months ago by ijpulidos
  1

• Error when trying to assign partial charges to the eg5 cofactor using openff-toolkit/openeye am1bccelf10

  #107 opened 7 months ago by hannahbaumann
  1

• Questions regarding specific ligands in the PLB

  #101 opened 10 months ago by hannahbaumann
  4

• Use OpenEye tools for pose generation/preparation?

  #105 opened 10 months ago by ijpulidos
  0

• Ring substituents for some ligands in different orientations, even though same substituent

  #104 opened 10 months ago by hannahbaumann
  1

• Include data from latest Schrodinger's public dataset

  #102 opened 10 months ago by ijpulidos
  0

• MCL-1 is not capped at C terminus?

  #75 opened a year ago by IAlibay
  3

• Check stability of ligand poses in long MD simulations

  #97 opened a year ago by jchodera
  0

• Add manually curated transformation network

  #96 opened a year ago by ijpulidos
  0

• doi listed for eg5 ligand data is incorrect

  #94 opened a year ago by dkozuch
  0

• structure of edges yamls

  #92 opened a year ago by richardjgowers
  2

• Remove old edges.yaml files, replace with new calculated ones

  #69 opened a year ago by IAlibay
  0

• Update of README.md Summary needed

  #90 opened 2 years ago by mvkrier
  2

• cMET only has 5 cmpds now

  #91 opened a year ago by bcossins
  2

• For CI, add PDB reading and FF application via OpenMM, ambertools (leap template) for all targets

  #89 opened 2 years ago by dotsdl
  0

• Investigate abnormal ligand conformations in CDK8

  #72 opened 2 years ago by IAlibay
  1

• Connectivity for NME caps is missing

  #88 opened 2 years ago by IAlibay
  1

• Fix PDB files

  #68 opened 2 years ago by IAlibay
  1

• YAML Schema

  #86 opened 2 years ago by mikemhenry
  1

• Abnormal ligand conformations

  #81 opened 2 years ago by IAlibay
  0

• Remove `.maegz` files from `main` history, if possible

  #85 opened 2 years ago by dotsdl
  0

• Thrombin PDB unusual residue indexes

  #84 opened 2 years ago by JSLJ23
  3

• SHP2 ligands have some suspect conformations

  #80 opened 2 years ago by Yoshanuikabundi
  2

• Restructure repo with `data` included within Python package

  #77 opened 2 years ago by dotsdl
  0

• Restructure `target.yml` schema to feature `primary` and `secondary` PDB structure keys

  #57 opened 2 years ago by dotsdl
  0

• Redesign Science re-curated benchmark

  #62 opened 2 years ago by jchodera
  1

• Link or store "known" computed results?

  #40 opened 2 years ago by IAlibay
  3

• Presence of two PDBs for Thrombin

  #71 opened 2 years ago by IAlibay
  2

• Update (or remove?) `targets.yaml` data file

  #70 opened 2 years ago by ijpulidos
  2

• Document changes to the PLB set

  #66 opened 2 years ago by IAlibay
  0

• Remove `cd2_ligs` directory and zip file in `cdk2`?

  #74 opened 2 years ago by IAlibay
  0

• Investigate clashes

  #73 opened 2 years ago by IAlibay
  2

• Fix Python API, CI, and remove "example" files

  #67 opened 2 years ago by IAlibay
  0

• Restructure repo to avoid need for LFS; drop LFS

  #53 opened 2 years ago by dotsdl
  5

• Generate benchmark data

  #65 opened 2 years ago by IAlibay
  1

• Store assay specific information in `targets.yaml`

  #59 opened 2 years ago by IAlibay
  4

• cannot process my ligand through tleap

  #61 opened 2 years ago by khelmy55
  1

• Inconsistencies between preparation and assay conditions

  #63 opened 2 years ago by IAlibay
  0

• Versioning

  #46 opened 2 years ago by richardjgowers
  3

• Protonation state of HIS248 in HIF2A needs to be adapted

  #64 opened 2 years ago by Gilli08
  1

• DOI for EG5 ligand measurements point to the wrong place

  #60 opened 2 years ago by IAlibay
  0

• Add branch protection for main?

  #49 opened 2 years ago by IAlibay
  3

• Add CITATION.cff file to match the Contributors information

  #44 opened 2 years ago by jchodera
  4

• Get RTD to build on PR builds

  #38 opened 2 years ago by IAlibay
  4

• Rename `master` branch to `main`?

  #41 opened 2 years ago by IAlibay
  1

• Remove LGTM

  #43 opened 2 years ago by mikemhenry
  1

• Long term discussion: move away from gromacs topologies

  #39 opened 2 years ago by IAlibay
  0