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Arcadia-Science
/
ProteinCartography
a pipeline to build similarity maps of protein space
MIT License
26
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10
forks
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[Sync] Pin arcadia-pycolor and update README
#89
keithchev
closed
1 month ago
0
When Running Demo Snakemake Crashes
#88
JooshK
closed
1 month ago
2
Missing file in `setup.py`
#87
alexj-lee
closed
1 month ago
2
[Sync] Reorganize output directories + deduplicate snakefiles + bugfixes
#86
keithchev
closed
3 months ago
0
Issue with tutorial snakemake
#85
vbx1404
opened
5 months ago
7
Replace BLAST search with mmseqs2
#84
naailkhan28
opened
7 months ago
1
Ensure user-provided PDBs are used for clustering
#83
keithchev
closed
7 months ago
0
`make_pdb` ESMFold jobs running even when input structure is provided
#82
naailkhan28
closed
7 months ago
8
Fix ESMFold API requests - disable SSL to avoid certificate errors
#81
naailkhan28
closed
7 months ago
4
ESMFold API for structure prediction is broken - won't work with SSL certificate checks
#80
naailkhan28
closed
7 months ago
1
Rc/0.4.2
#79
keithchev
closed
8 months ago
0
hover text not showing for some proteins
#78
kevinkoh09
opened
9 months ago
1
Request to add Taxon info to hovertext box
#75
scienceYeeSu
opened
9 months ago
0
Long protein names cut off info in hovertext box
#74
scienceYeeSu
closed
7 months ago
2
Minor bug fixes
#73
mertcelebi
closed
9 months ago
0
AttributeError: 'NoneType' object has no attribute 'services'
#72
jasbneal
closed
7 months ago
2
A question
#71
ValWood
closed
10 months ago
2
consider adding resource execution settings to `config.yml`
#70
taylorreiter
closed
7 months ago
1
Add configuration to support Snakemake parallelization
#69
lebovic
closed
10 months ago
1
ESMfold vs AF pLDDT
#68
borgesadair1
closed
11 months ago
1
Optionality not to use BLAST
#67
borgesadair1
opened
11 months ago
1
snakemake errors running demo
#66
kylekimler
closed
11 months ago
5
Multiple key proteins fails at plot_interactive.py
#64
braebigge
closed
7 months ago
1
Add in exponential backoff of API calls.
#63
neevor
closed
11 months ago
1
.faa files fail in search mode
#62
borgesadair1
closed
7 months ago
3
Create feature matrix without using pivot table.
#61
neevor
closed
11 months ago
5
Adding requests header, minor documentation updates
#60
mezarque
closed
11 months ago
0
Remove Nextflow scaffolding for now
#59
mertcelebi
closed
11 months ago
0
Mean pLDDT is 0-1 for Esmfold
#57
borgesadair1
closed
7 months ago
1
PDBorigin field doesnt have ESMfold info
#56
borgesadair1
closed
7 months ago
1
Automated testing
#55
mezarque
closed
7 months ago
1
Linting scripts
#53
mezarque
closed
11 months ago
1
Hover text on visualization sometimes obscures the majority of the scatterplot
#51
ilyakolb
closed
7 months ago
4
Implement TM-score fill-in for missing data relative to inputs
#50
mezarque
closed
3 months ago
1
Memory usage in foldseek_clustering.py
#49
jasegehring
closed
11 months ago
4
Clarification to README when running on AWS
#47
ilyakolb
closed
11 months ago
2
Issue downloading proteins from AlphaFold
#44
mezarque
closed
7 months ago
0
Das/byebyebioservices
#39
mezarque
closed
11 months ago
9
Proteins duplicated in the results in "From Query" version of the pipeline
#38
braebigge
closed
11 months ago
1
Randomness/incompleteness of API calls?
#35
elizabethmcd
closed
1 year ago
4
Add parameter for user to define hits must be certain % of the length of the reference protein to include in results
#34
elizabethmcd
closed
11 months ago
2
Simple semantic analysis plots
#31
mezarque
closed
11 months ago
2
feature request- add percent sequence identity to output aggregated features file
#30
ecpierce
closed
7 months ago
4
Init nextflow scaffold
#29
mertcelebi
closed
1 year ago
0
Feature request for assessment of input .pdb quality
#28
ecpierce
opened
1 year ago
3
Add an overlay to show how similar proteins are to the input protein
#22
braebigge
closed
1 year ago
1
Consider removing structural cluster overlay
#21
braebigge
closed
1 year ago
1
Add metrics for looking at the difference between clusters
#20
braebigge
closed
1 year ago
1
Add metrics about the quality of the protein fold predictions
#19
braebigge
closed
11 months ago
1
Create version of pipeline that starts with predefined list of structures/ proteins
#18
mezarque
closed
1 year ago
1
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