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HannesStark
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EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
MIT License
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Question regarding how to extract protein representation from your pretrain model
#74
Tizzzzy
opened
1 month ago
0
It takes forever to load checkpoint
#73
hnguyentt
closed
1 month ago
0
the original purpose and actual effect of reduce_receptors.py script file
#72
tangmaomao16
opened
2 months ago
0
pyaml syntax error
#71
BlackWyvernX
opened
3 months ago
1
Why use openbabel in data preprocessing
#70
tangmaomao16
closed
4 months ago
1
dgl.copy_edge deprecated
#69
benjileibo
opened
1 year ago
2
packages missing
#68
benjileibo
opened
1 year ago
0
Update equibind.py
#67
Eshan-Yadav
opened
1 year ago
0
Blind Docking - Using the whole protein or only just part of protein
#66
lkqnaruto
closed
4 months ago
1
About the Training Efficiency
#65
youqingxiaozhua
closed
1 year ago
1
about dgllife version and usage
#64
lichman0405
closed
1 year ago
1
How to continue a training from the checkpoint
#63
Nailo
closed
2 years ago
2
Keep getting the OSError
#62
Nailo
closed
2 years ago
1
Conformations are being sampled even with use_rdkit_coords=False
#61
jadolfbr
closed
2 years ago
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
RishalAggarwal
closed
2 years ago
1
Torch not compiled with CUDA enabled
#59
taliaora
closed
2 years ago
0
Missing psutil dependency
#58
GrayWasTaken
closed
1 year ago
1
Fix for #46 and updates to internal ligand loading
#57
amfaber
opened
2 years ago
0
About hydrogen removement
#56
KruskalLin
closed
2 years ago
0
Add device check before multiligand inference
#55
zahidpanj
closed
2 years ago
0
Add psutil to environment.yml
#54
zahidpanj
closed
2 years ago
0
c
#53
monabiyan
closed
2 years ago
1
Is is possible to predict torsion angle directly from model?
#52
lkfo415579
closed
1 year ago
1
EquiBind result analysis
#51
PhungVanDuy
closed
2 years ago
1
psutils error
#50
monabiyan
closed
2 years ago
2
reproduction of paper results and ligand/protein prep
#49
abazabaaa
closed
2 years ago
1
Choice of binding site or whole protein docking?
#48
Tonylac77
closed
2 years ago
1
CUDA error
#47
mrinal-shekhar
closed
1 year ago
3
Torch not compiled with CUDA enabled
#46
struggle007
closed
1 year ago
4
Multiple GPUs
#45
Harry4FunResearch
closed
2 years ago
1
Questions about RDKit conformer generation, fast point cloud conformer fitting, and EquiBind-R meaning.
#44
yufengwhy
closed
1 year ago
3
Ignore .DS_Store
#43
kjwallace
closed
2 years ago
0
Questions about reproducing
#42
lijiashan2020
closed
2 years ago
2
Bad Clashes
#41
jadolfbr
closed
2 years ago
3
Questions about SE(3)-equivariant
#40
Surviveagainsttheodds
closed
2 years ago
4
invalid value in pickle
#39
yufengwhy
closed
2 years ago
3
Does current models supported multiple suggestion outputs?
#38
PhungVanDuy
closed
2 years ago
6
Support for inference on multiple ligands in sdf and smi formats
#37
amfaber
closed
2 years ago
4
Scale off for results
#36
jadolfbr
closed
2 years ago
6
Can't Kekulize mol
#35
jadolfbr
closed
2 years ago
3
Inference should be able to be run from any directory?
#34
jadolfbr
closed
2 years ago
2
Hydrogens on receptors
#33
amfaber
closed
2 years ago
3
Baseline details, global docking configuration, GLIDE.
#32
luwei0917
closed
2 years ago
1
Can't kekulize mol. Unkekulized atoms
#31
Harry4FunResearch
closed
2 years ago
2
Corrected SDF files positions appear to be incorrect
#30
dinsausti
closed
2 years ago
2
Memory requirements for training?
#29
neild0
closed
2 years ago
1
Support for multiple random rdkit confirmations for each ligand
#28
dylanabramson33
closed
2 years ago
3
Calculating corrected intersection losses at inference
#27
J-Salo
closed
2 years ago
2
Can you provide the training config file for re-docking setting ?
#26
PhungVanDuy
closed
2 years ago
1
142 instead 144 new receptors.
#25
luwei0917
closed
2 years ago
3
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