https://github.com/biocomputingup/caid-reference
Critical Assessment of Protein Intrinsic Disorder (CAID) - Reference generation and analysis
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: ncbi.nlm.nih.gov -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.8%) to scientific vocabulary
Repository
Critical Assessment of Protein Intrinsic Disorder (CAID) - Reference generation and analysis
Basic Info
- Host: GitHub
- Owner: BioComputingUP
- License: gpl-3.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 22.3 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Critical Assessment of Protein Intrinsic Disorder (CAID)
This is the official repository of the Critical Assessment of Protein Intrinsic Disorder (CAID) challenge.
The previous CAID2 repository is available here.
Follow the instructions below to replicate the generation of the references and some useful statistics.
```bash
Generate the folder structure
mkdir -p data/{disprot,sifts,alphafold,output/{references,referencesstat,referencesmergeanalysis,homology,newtaxdump}} ````
references
Generate the references from two snapshots of the DisProt database (mongo export) DisProt data can be obtained directly exporting the relevant database collections (ask the developers). Or using the download service from the website (lastest annotations might not be available to the public). Note the formats are slightly different.
Download DisProt data
Use MongoDB compass and download the current public collection and the current "curators" collections.
- Public 2024_12 # public at the time predictors submitted their software
- Current 202506c # 1 July 2025, 15:55 CEST
To download directly from MongoDB with a command (e.g. CAID3 CASP-16 dataset) mongoexport --uri "mongodb://moros:27017/disprot8" --collection entries202506c > data/disprot/disprot8.entries202506c.json
references_stat
Generate statistics about the references
homology
Parse the blast output, extract information about the best match and perform optimal pairwise alignments. Comparison are between CAID and DisProt "old" and between CAID and PDB seqres.
```bash
Download SIFTS data to get the list of SEQRES sequences in the PDB
wget -O data/sifts/uniprotsegmentsobserved.tsv.gz ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/flatfiles/tsv/uniprotsegmentsobserved.tsv.gz wget -O data/disprot/go-basic.obo http://purl.obolibrary.org/obo/go/go-basic.obo
Generate BLAST alignments of the new DisProt against the old DisProt and against PDB seqres
Install blast on your home (check the version and paths)
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.15.0+-x64-linux.tar.gz tar -xf ncbi-blast-2.15.0+-x64-linux.tar.gz export PATH="/home/$USER/ncbi-blast-2.15.0+/bin:$PATH"
Download PDB seqres
wget https://files.wwpdb.org/pub/pdb/deriveddata/pdbseqres.txt.gz -O data/output/homology/pdbseqres.txt.gz gunzip data/output/homology/pdbseqres.txt.gz
Make blast dbs
makeblastdb -in data/output/homology/disprotold.fasta -dbtype prot makeblastdb -in data/output/homology/pdbseqres.txt -dbtype prot
Run BLAST
blastp -db data/output/homology/disprotold.fasta -query data/output/homology/disprotnew.fasta -out data/output/homology/disprotnewold.blast -outfmt 6 -numthreads 12 blastp -db data/output/homology/pdbseqres.txt -query data/output/homology/disprotnew.fasta -out data/output/homology/disprotnewpdb.blast -outfmt 6 -numthreads 12 ```
homology_plot
Generate plots from the output of the homology notebook
```bash
Download taxonomy data
wget -O data/newtaxdump.tar.gz ftp://ftp.ncbi.nih.gov/pub/taxonomy/newtaxdump/newtaxdump.tar.gz tar -xf data/newtaxdump.tar.gz -C data/new_taxdump ```
references_merge
Combine predictions with reference data. It requires the predictions, the references, the mapping of predictions to the different challenges and the assessment (F1-score) one for each reference
referencemergeanalysis
Generate figures comparing predictions and references, one for each target
Owner
- Name: BioComputing Group, University of Padova
- Login: BioComputingUP
- Kind: organization
- Email: biocomp@bio.unipd.it
- Location: Italy
- Website: https://biocomputingup.it/
- Repositories: 31
- Profile: https://github.com/BioComputingUP
GitHub Events
Total
- Push event: 2
- Create event: 2
Last Year
- Push event: 2
- Create event: 2
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Damiano Piovesan | d****n@g****m | 3 |
Issues and Pull Requests
Last synced: about 1 year ago
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Past Year
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