BorgwardtLab/proteinshake

Issues

• Miss match of sequence length, residue_number and residue_type

  #274 opened 6 months ago by zpengmei
  4

• Structure Similarity Task training

  #273 opened 8 months ago by ahariri13
  1

• Dependency on rdkit-pypi prevents installation of version above 0.2.1

  #272 opened 8 months ago by luiswyss
  1

• Integrate time benchmarking for transforms

  #271 opened 9 months ago by timkucera
  0

• Handling of multiple rotamers in PDB files

  #270 opened 9 months ago by lucasmiranda42
  2

• preprocessing: relaxation

  #269 opened 9 months ago by timkucera
  0

• Structure Relaxation

  #268 opened 10 months ago by timkucera
  0

• Could you provide the script for building structure-similarity splits?

  #267 opened a year ago by LTEnjoy
  1

• Type of Family Classification Dataset

  #266 opened a year ago by mahdip72
  1

• Pfam labels

  #254 opened a year ago by timkucera
  1

• Substrate/Product data for Enzymes

  #265 opened a year ago by jozhang97
  2

• Add drug-target interaction task

  #264 opened a year ago by pjhartout
  0

• schedule test workflows regularly

  #262 opened a year ago by timkucera
  0

• replace str.rstrip with str.removesuffix

  #261 opened a year ago by timkucera
  0

• web server API to backend

  #259 opened a year ago by timkucera
  0

• operations on datasets

  #258 opened a year ago by cgoliver
  0

• db: https://intenzydb.accre.vanderbilt.edu/

  #257 opened a year ago by timkucera
  0

• docs: search broken

  #256 opened a year ago by timkucera
  0

• QC

  #255 opened a year ago by timkucera
  0

• PDB substructure selection

  #253 opened a year ago by cgoliver
  0

• .citation(format) method as part of the dataset

  #252 opened a year ago by timkucera
  1

• migrate leaderboard to paperswithcode

  #219 opened 2 years ago by timkucera
  1

• checkpoint conversions

  #251 opened a year ago by timkucera
  0

• automatically generate a leaderboard entry

  #247 opened a year ago by timkucera
  1

• set up organization

  #246 opened a year ago by timkucera
  0

• add FLOPs and parameter metrics to task

  #245 opened a year ago by timkucera
  0

• records downloads of datasets

  #244 opened a year ago by timkucera
  0

• frameworks in docs

  #228 opened a year ago by timkucera
  1

• sort all globs

  #242 opened a year ago by timkucera
  0

• Check edge_attribute in pyg()

  #241 opened a year ago by cgoliver
  0

• domain

  #240 opened a year ago by timkucera
  0

• Website mobile-friendly

  #239 opened a year ago by timkucera
  0

• Dataset and Task documentation

  #237 opened 2 years ago by timkucera
  0

• quality scores and filtering

  #217 opened 2 years ago by timkucera
  0

• Check DUDE

  #238 opened 2 years ago by timkucera
  0

• sharded avros

  #227 opened 2 years ago by timkucera
  0

• double check all tasks

  #230 opened 2 years ago by timkucera
  0

• add label distributions to docs

  #231 opened 2 years ago by timkucera
  0

• get ID from pdb header instead of filename?

  #233 opened 2 years ago by timkucera
  0

• add back tutorials to docs

  #232 opened 2 years ago by timkucera
  0

• improve warnings

  #234 opened 2 years ago by timkucera
  0

• ProteinShake DataLoader?

  #236 opened 2 years ago by timkucera
  0

• cleanup code and docstrings

  #226 opened 2 years ago by timkucera
  0

• rewrite task class

  #223 opened 2 years ago by timkucera
  0

• ditch AF organisms

  #225 opened 2 years ago by timkucera
  0

• tests: mock download_url in test_preprocess instead of other methods

  #229 opened 2 years ago by timkucera
  0

• switch to `use_precomputed=False` if dataset not available

  #222 opened 2 years ago by timkucera
  0

• add secondary structure as a feature to residues/atoms

  #220 opened 2 years ago by timkucera
  0

• switch completely to UniProt

  #221 opened 2 years ago by timkucera
  0

• modularized filtering pipeline

  #218 opened 2 years ago by timkucera
  0