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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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multiple CVs for the splits
#175
timkucera
opened
1 year ago
0
GeneOntologyTask Smin metric
#174
timkucera
opened
1 year ago
0
filter EC dataset for multiple EC classes
#173
timkucera
opened
1 year ago
0
only filter pdb models if NMR structure
#172
timkucera
opened
1 year ago
0
Clustersplits
#171
timkucera
closed
1 year ago
0
Preprint tasks
#170
cgoliver
closed
1 year ago
3
simple visualization for graph, voxel, point clouds
#169
timkucera
opened
1 year ago
1
automated pypi update linked to main branch
#168
timkucera
closed
1 year ago
0
Add UniProt annotations to AlphaFold datasets
#167
timkucera
closed
1 year ago
1
pretrain task
#166
timkucera
opened
1 year ago
0
accept list of pdbs in RCSBDataset.download_from_rcsb
#165
timkucera
closed
1 year ago
1
add 'year' attribute to proteins
#164
cgoliver
opened
1 year ago
0
update dependencies
#163
timkucera
closed
1 year ago
1
adjust github settings for submission
#162
timkucera
closed
1 year ago
0
add licenses
#161
timkucera
closed
1 year ago
0
Examples
#160
claying
closed
1 year ago
1
function (label) based splits
#159
timkucera
opened
1 year ago
0
protein backbone angles
#158
cgoliver
opened
1 year ago
0
Add __getitem__ to base dataset class
#157
timkucera
opened
1 year ago
2
Task splits based on sequence clusters
#156
timkucera
closed
1 year ago
1
Rewrite check_attributes_same_as_hosted
#155
timkucera
closed
1 year ago
1
Option for TMalign to return aligned structures
#154
cgoliver
closed
1 year ago
3
Build system move to pyproject.toml
#153
pjhartout
opened
1 year ago
0
Code style enforcement
#152
pjhartout
opened
1 year ago
1
Code style enforcement
#151
pjhartout
closed
1 year ago
2
Fix typo in coverage
#150
pjhartout
closed
1 year ago
0
use biopandas API for saving PDBs
#149
cgoliver
closed
1 year ago
1
Add test coverage
#148
pjhartout
closed
1 year ago
2
Check which PDBs have already been downloaded in RCSBDataset
#147
timkucera
opened
1 year ago
0
Use biopandas API to extract sequence
#146
cgoliver
opened
1 year ago
0
Migrate to zenodo production repository
#145
pjhartout
closed
1 year ago
0
Website
#144
timkucera
closed
1 year ago
0
add proxies for dataset functions in task api
#143
timkucera
closed
1 year ago
1
multi-chain sequence
#142
cgoliver
opened
1 year ago
0
cd-hit drops some sequences
#141
timkucera
closed
1 year ago
1
NaN clustering for TM scores
#140
timkucera
closed
1 year ago
1
Verbosity in Dataset class
#139
timkucera
closed
1 year ago
0
Precompute surfaces
#138
timkucera
closed
1 year ago
1
Integrate C dependencies
#137
timkucera
closed
1 year ago
2
Slow down RCSB download if request limit is reached
#136
timkucera
opened
1 year ago
0
Labelled datasets with AlphaFold proteins
#135
timkucera
opened
1 year ago
0
Cache TM-score calculations
#134
timkucera
closed
1 year ago
0
tm score caching, word size adjust, rename distance to similarity
#133
cgoliver
closed
1 year ago
5
allow multiple distance thresholds in clustering
#132
cgoliver
closed
1 year ago
0
kill stale/abandoned branches
#131
cgoliver
closed
1 year ago
0
sequence and structure-based clustering
#130
cgoliver
closed
1 year ago
0
Compute structure and sequence-based splits for all tasks
#129
cgoliver
closed
1 year ago
1
Transforms subpackage + surface computation
#128
cgoliver
closed
1 year ago
0
add TMalign on all pairs in dataset class
#127
cgoliver
closed
1 year ago
0
tokenizer issue with atom resolution
#126
cgoliver
closed
1 year ago
3
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