HannesStark/EquiBind

Issues

• Question regarding how to extract protein representation from your pretrain model

  #74 opened 4 months ago by Tizzzzy
  0

• It takes forever to load checkpoint

  #73 opened 4 months ago by hnguyentt
  0

• Keep getting the OSError

  #62 opened 2 years ago by Nailo
  1

• the original purpose and actual effect of reduce_receptors.py script file

  #72 opened 6 months ago by tangmaomao16
  0

• pyaml syntax error

  #71 opened 7 months ago by BlackWyvernX
  1

• Blind Docking - Using the whole protein or only just part of protein

  #66 opened 7 months ago by lkqnaruto
  1

• Why use openbabel in data preprocessing

  #70 opened 7 months ago by tangmaomao16
  1

• dgl.copy_edge deprecated

  #69 opened 2 years ago by benjileibo
  2

• packages missing

  #68 opened 2 years ago by benjileibo
  0

• About the Training Efficiency

  #65 opened 2 years ago by youqingxiaozhua
  1

• about dgllife version and usage

  #64 opened 2 years ago by lichman0405
  1

• Missing psutil dependency

  #58 opened 2 years ago by GrayWasTaken
  1

• Is is possible to predict torsion angle directly from model?

  #52 opened 2 years ago by lkfo415579
  1

• CUDA error

  #47 opened 2 years ago by mrinal-shekhar
  3

• Torch not compiled with CUDA enabled

  #46 opened 2 years ago by struggle007
  4

• Questions about RDKit conformer generation, fast point cloud conformer fitting, and EquiBind-R meaning.

  #44 opened 2 years ago by yufengwhy
  3

• How to continue a training from the checkpoint

  #63 opened 2 years ago by Nailo
  2

• c

  #53 opened 2 years ago by monabiyan
  1

• Conformations are being sampled even with use_rdkit_coords=False

  #61 opened 2 years ago by jadolfbr
  2

• Hey, I'm trying to retrain the equibind model but I think I keep getting oom when processing the dataset, specifically in the "Get receptors, filter chains, and get its coordinates" step. I'm hoping you can tell me how much memory is required for this step and if there's a way around it. I'm training on the PDBBind dataset you have provided.

  #60 opened 2 years ago by RishalAggarwal
  1

• Torch not compiled with CUDA enabled

  #59 opened 2 years ago by taliaora
  0

• EquiBind result analysis

  #51 opened 2 years ago by PhungVanDuy
  1

• reproduction of paper results and ligand/protein prep

  #49 opened 2 years ago by abazabaaa
  1

• psutils error

  #50 opened 2 years ago by monabiyan
  2

• Multiple GPUs

  #45 opened 2 years ago by Harry4FunResearch
  1

• Choice of binding site or whole protein docking?

  #48 opened 2 years ago by Tonylac77
  1

• About hydrogen removement

  #56 opened 2 years ago by KruskalLin
  0

• Bad Clashes

  #41 opened 3 years ago by jadolfbr
  3

• Does current models supported multiple suggestion outputs?

  #38 opened 3 years ago by PhungVanDuy
  6

• Questions about SE(3)-equivariant

  #40 opened 3 years ago by Surviveagainsttheodds
  4

• Questions about reproducing

  #42 opened 3 years ago by lijiashan2020
  2

• Scale off for results

  #36 opened 3 years ago by jadolfbr
  6

• invalid value in pickle

  #39 opened 3 years ago by yufengwhy
  3

• Can't kekulize mol. Unkekulized atoms

  #31 opened 3 years ago by Harry4FunResearch
  2

• Can't Kekulize mol

  #35 opened 3 years ago by jadolfbr
  3

• Inference should be able to be run from any directory?

  #34 opened 3 years ago by jadolfbr
  2

• Hydrogens on receptors

  #33 opened 3 years ago by amfaber
  3

• Baseline details, global docking configuration, GLIDE.

  #32 opened 3 years ago by luwei0917
  1

• Corrected SDF files positions appear to be incorrect

  #30 opened 3 years ago by dinsausti
  2

• Memory requirements for training?

  #29 opened 3 years ago by neild0
  1

• 142 instead 144 new receptors.

  #25 opened 3 years ago by luwei0917
  3

• Can you provide the training config file for re-docking setting ?

  #26 opened 3 years ago by PhungVanDuy
  1

• Support for multiple random rdkit confirmations for each ligand

  #28 opened 3 years ago by dylanabramson33
  3

• Calculating corrected intersection losses at inference

  #27 opened 3 years ago by J-Salo
  2

• Measure of inference quality

  #24 opened 3 years ago by hmms117
  4

• FileNotFoundError: train_arguments.yaml

  #23 opened 3 years ago by Tonylac77
  6

• Does EquiBind supports given binding site?

  #22 opened 3 years ago by jooewood
  1

• ValueError: list.remove(x): x not in list in process_mols.py line 692, in get_geometry_graph

  #21 opened 3 years ago by moritzschaefer
  2

• Error when run get_receptor_inference

  #20 opened 3 years ago by SejeongPark8354
  6

• [Question] Graph representations

  #19 opened 3 years ago by rhjohnstone
  1