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BorgwardtLab
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proteinshake
Protein structure datasets for machine learning.
https://proteinshake.ai
BSD 3-Clause "New" or "Revised" License
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Splits
#75
timkucera
closed
2 years ago
0
OffMemory Datasets
#74
timkucera
closed
2 years ago
0
Parallelize representation conversion (graph,voxel,point,...)
#73
timkucera
opened
2 years ago
0
Write tests for all representations and frameworks
#72
timkucera
closed
2 years ago
1
Add PPI and PLI info to atom level
#71
timkucera
closed
2 years ago
0
Website
#70
timkucera
closed
1 year ago
1
Custom filters
#69
timkucera
opened
2 years ago
2
Stream into file during parsing
#68
timkucera
opened
2 years ago
0
New format
#67
timkucera
closed
2 years ago
1
Parallel parsing does not work
#66
timkucera
closed
1 year ago
2
lazy loading of proteins object
#65
timkucera
closed
2 years ago
0
replace all 'torch-pdb' references in code and docs
#64
timkucera
closed
2 years ago
0
Bug with "residue_index" attribute
#63
claying
closed
2 years ago
1
Add edge features in graphs (backbone/not-backbone)
#62
timkucera
opened
2 years ago
2
Remove the unzipping step and unzipped file for faster processing.
#61
claying
closed
2 years ago
1
Add 1D embedding of residue identity
#60
cgoliver
closed
2 years ago
0
Fix pickling bug when n_workers > 1
#59
cgoliver
closed
2 years ago
0
Make one-hot encoding of residue number optional
#58
cgoliver
closed
2 years ago
1
num_workers > 1
#57
cgoliver
closed
2 years ago
4
Train example models to show effect of pretraining
#56
timkucera
closed
2 years ago
2
Add filter function to exclude a list of PDBs
#55
timkucera
closed
2 years ago
0
Add AlphaFold scores to the protein object
#54
timkucera
closed
2 years ago
0
New dataset with "confident" AlphaFold predictions
#53
timkucera
closed
2 years ago
1
Docs rename
#52
cgoliver
closed
2 years ago
0
think about data storage again
#51
timkucera
closed
2 years ago
0
Rebuild docs with new name & make sure up to date
#50
cgoliver
closed
1 year ago
2
rename
#49
timkucera
closed
2 years ago
1
AlphaFold Dataset with custom list of IDs
#48
timkucera
opened
2 years ago
0
Ignore proteins when too small
#47
cgoliver
closed
2 years ago
0
Double check protein structures and sequences
#46
timkucera
opened
2 years ago
0
Dataset creation crashes on GODataset k=5 graph
#45
cgoliver
closed
2 years ago
4
uncompress after download
#44
timkucera
closed
2 years ago
0
get number of proteins in total for data summary
#43
cgoliver
closed
1 year ago
1
Implement point cloud and voxel representations
#42
timkucera
closed
2 years ago
0
compose embeddings
#41
timkucera
closed
2 years ago
0
Dev tim
#40
timkucera
closed
2 years ago
0
remove compression after download
#39
timkucera
closed
2 years ago
0
licenses
#38
timkucera
closed
2 years ago
0
update readme and doc landing page
#37
timkucera
closed
2 years ago
0
check dgl
#36
timkucera
closed
2 years ago
4
include all atoms in base dataset class
#35
cgoliver
closed
2 years ago
0
fix pdbbind bugs on 'frameworks' branch
#34
cgoliver
closed
2 years ago
0
Protein structure descriptor module.
#33
cgoliver
opened
2 years ago
3
add access to raw PDB in Datasets
#32
cgoliver
closed
2 years ago
1
Frameworks
#31
timkucera
closed
2 years ago
1
launch AF and PDBbindPPI precompute + release
#30
cgoliver
closed
2 years ago
0
Add contribution instructions to the readme
#29
timkucera
closed
1 year ago
1
Alphafold
#28
timkucera
closed
2 years ago
0
Add point cloud support
#27
cgoliver
closed
2 years ago
1
dynamic frameworking
#26
timkucera
closed
2 years ago
0
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