https://github.com/haddocking/arctic3d
Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
https://github.com/haddocking/arctic3d
clustering data-mining data-retrieval macromolecular-modeling pdbe-s-rest-api protein-docking utrecht-university
Last synced: 5 months ago
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Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
- Host: GitHub
- URL: https://github.com/haddocking/arctic3d
- Owner: haddocking
- License: apache-2.0
- Created: 2022-06-30T12:12:44.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-12-03T15:05:11.000Z (7 months ago)
- Last Synced: 2025-12-06T19:49:44.368Z (7 months ago)
- Topics: clustering, data-mining, data-retrieval, macromolecular-modeling, pdbe-s-rest-api, protein-docking, utrecht-university
- Language: Python
- Homepage:
- Size: 1.99 MB
- Stars: 32
- Watchers: 12
- Forks: 6
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
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README
# ARCTIC-3D
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**A**utomatic **R**etrieval and **C**lus**T**ering of **I**nterfaces in Complexes from **3D** structural information
## WEB SERVER
ARCTIC-3D is available at this webserver https://wenmr.science.uu.nl/arctic3d/
## ARCTIC-3D: all you want to know about protein-specific interfaces
ARCTIC-3D is a software for data-mining and clustering of protein interface information. It allows you to retrieve all the existing interface information for your desired protein from the PDBE graph database (https://www.ebi.ac.uk/pdbe/pdbe-kb/), grouping similar interfaces in interacting surfaces.
The software first checks your input (a uniprot ID, a FASTA file, or a PDB file), and then retrieves the existing interaction data from the [graph API](https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/). Such interfaces are projected on a selected PDB structure and their dissimilarity is calculated, thus allowing for the application of a hierarchical clustering algorithm.
In output you will see how your favourite protein can display different binding surfaces, each one characterised by few residues that are always present (_hotspots_) and other amino acids which are at the interface only from time to time.
## Developing
Check [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
## Installation
### With `conda`
Clone the repository on your computer and navigate to it
```bash
git clone git@github.com:haddocking/arctic3d.git
cd arctic3d
```
Here you can create the arctic3d environment:
```bash
conda create -n arctic3d python=3.10
conda activate arctic3d
pip install .
arctic3d -h
```
## To run BLAST locally
```bash
bash install_blast_deps.sh
```
And put `blastp` in your `$PATH` by adding the following line to your `.bashrc` or `.bash_profile` file:
```bash
export PATH="PATH_TO_YOUR_ARCTIC3D_INSTALLATION/src/ncbi-blast-2.15.0+/bin:$PATH"
```
## Example usage
Please refer to the [examples](docs/examples.md) documentation page.
## Detailed documentation
In order to generate a detailed html documentation please execute these commands
```text
pip install myst_parser
pip install chardet
conda install sphinx
sphinx-build -E docs ./arctic3d-docs
```
Then you can open the file `arctic3d-docs/index.html`, which contains all the necessary documentation.
## Citing us
If you used ARCTIC-3D in your work please cite the following publication:
**Marco Giulini, Rodrigo V. Honorato, Jesús L. Rivera, and Alexandre MJJ Bonvin**: "ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information." Communications Biology 7, no. 1 (2024): 49. (www.nature.com/articles/s42003-023-05718-w)