| Name | arctic3d JSON |
| Version |
0.4.1
JSON |
| download |
| home_page | None |
| Summary | Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information |
| upload_time | 2024-04-22 12:14:07 |
| maintainer | None |
| docs_url | None |
| author | BonvinLab |
| requires_python | <3.12,>=3.9 |
| license | Apache-2.0 |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# ARCTIC-3D
[](https://github.com/haddocking/arctic3d/actions/workflows/ci.yml)
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<img src="https://raw.githubusercontent.com/haddocking/arctic3d/main/docs/imgs/arctic3d.png" width="450">
**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)
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"description": "# ARCTIC-3D\n\n[](https://github.com/haddocking/arctic3d/actions/workflows/ci.yml)\n[](https://www.codacy.com/gh/haddocking/arctic3d/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/arctic3d&utm_campaign=Badge_Coverage)\n[](https://www.codacy.com/gh/haddocking/arctic3d/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/arctic3d&utm_campaign=Badge_Grade)\n[](https://api.eu.badgr.io/public/assertions/oAuS52pQTWaC90qMk97hlA \"SQAaaS bronze badge achieved\")\n[](https://fair-software.eu)\n\n[](https://api.eu.badgr.io/public/assertions/oAuS52pQTWaC90qMk97hlA \"SQAaaS bronze badge achieved\")\n\n<img src=\"https://raw.githubusercontent.com/haddocking/arctic3d/main/docs/imgs/arctic3d.png\" width=\"450\">\n\n**A**utomatic **R**etrieval and **C**lus**T**ering of **I**nterfaces in Complexes from **3D** structural information\n\n## WEB SERVER\n\nARCTIC-3D is available at this webserver https://wenmr.science.uu.nl/arctic3d/\n\n## ARCTIC-3D: all you want to know about protein-specific interfaces\n\nARCTIC-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.\n\nThe 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.\n\nIn 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.\n\n## Developing\n\nCheck [CONTRIBUTING.md](CONTRIBUTING.md) for more information.\n\n## Installation\n\n### With `conda`\n\nClone the repository on your computer and navigate to it\n\n```bash\ngit clone git@github.com:haddocking/arctic3d.git\ncd arctic3d\n```\n\nHere you can create the arctic3d environment:\n\n```bash\nconda create -n arctic3d python=3.10\nconda activate arctic3d\npip install .\narctic3d -h\n```\n\n## To run BLAST locally\n\n```bash\nbash install_blast_deps.sh\n```\n\nAnd put `blastp` in your `$PATH` by adding the following line to your `.bashrc` or `.bash_profile` file:\n\n```bash\nexport PATH=\"PATH_TO_YOUR_ARCTIC3D_INSTALLATION/src/ncbi-blast-2.15.0+/bin:$PATH\"\n```\n\n## Example usage\n\nPlease refer to the [examples](docs/examples.md) documentation page.\n\n## Detailed documentation\n\nIn order to generate a detailed html documentation please execute these commands\n\n```text\npip install myst_parser\npip install chardet\nconda install sphinx\nsphinx-build -E docs ./arctic3d-docs\n```\n\nThen you can open the file `arctic3d-docs/index.html`, which contains all the necessary documentation.\n\n## Citing us\n\nIf you used ARCTIC-3D in your work please cite the following publication:\n\n**Marco Giulini, Rodrigo V. Honorato, Jes\u00fas 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)\n",
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