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arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

https://github.com/haddocking/arctic3d

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: nature.com, zenodo.org
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    Scientific vocabulary similarity
    Low similarity (11.1%) to scientific vocabulary

Keywords

clustering data-mining data-retrieval macromolecular-modeling pdbe-s-rest-api protein-docking utrecht-university
Last synced: 6 months ago · JSON representation ·

Repository

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

Basic Info
  • Host: GitHub
  • Owner: haddocking
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 1.99 MB
Statistics
  • Stars: 30
  • Watchers: 13
  • Forks: 6
  • Open Issues: 10
  • Releases: 7
Topics
clustering data-mining data-retrieval macromolecular-modeling pdbe-s-rest-api protein-docking utrecht-university
Created over 3 years ago · Last pushed 7 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

ARCTIC-3D

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Automatic Retrieval and ClusTering of Interfaces 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. 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 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 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)

Owner

  • Name: HADDOCK
  • Login: haddocking
  • Kind: organization
  • Location: Utrecht, The Netherlands

Computational Structural Biology Group @ Utrecht University

Citation (CITATION.cff) 

# YAML 1.2
# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
cff-version: 1.0.3
message: If you use this software, please cite it using these metadata.
# FIXME title as repository name might not be the best name, please make human readable
title: 'haddocking/arctic3d: v0.5.1'
doi: 10.5281/zenodo.10839520
# FIXME splitting of full names is error prone, please check if given/family name are correct
authors:
- given-names: Marco
  family-names: Giulini
  affiliation: Utrecht University
- given-names: Rodrigo
  family-names: Honorato
  name-particle: Vargas
  affiliation: '@UtrechtUniversity'
- given-names: Aldo
  family-names: van den Nieuwendijk
  affiliation:
- given-names: Alexandre
  family-names: Bonvin
  affiliation: '@UtrechtUniversity'
- given-names: Anton
  family-names: Bushuiev
  affiliation: Czech Technical University in Prague
version: 0.5.1
date-released: 2024-03-19
repository-code: https://github.com/haddocking/arctic3d
license: cc-by-4.0

GitHub Events

Total
  • Watch event: 2
  • Delete event: 31
  • Issue comment event: 10
  • Push event: 64
  • Pull request review event: 24
  • Pull request event: 59
  • Create event: 35
Last Year
  • Watch event: 2
  • Delete event: 31
  • Issue comment event: 10
  • Push event: 64
  • Pull request review event: 24
  • Pull request event: 59
  • Create event: 35

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 29
  • Average time to close issues: N/A
  • Average time to close pull requests: 19 days
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.21
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 29
Past Year
  • Issues: 0
  • Pull requests: 29
  • Average time to close issues: N/A
  • Average time to close pull requests: 19 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.21
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 29
View more stats
Top Authors
Issue Authors
  • rvhonorato (6)
  • mgiulini (3)
  • roxanavas (1)
  • dependabot[bot] (1)
Pull Request Authors
  • dependabot[bot] (92)
  • rvhonorato (8)
  • mgiulini (6)
  • VGPReys (1)
Top Labels
Issue Labels
dependencies (5) bug (2) refactor (2) community (2) documentation (1) tests (1)
Pull Request Labels
dependencies (96) python (15) tests (4) bug (2) community (2) refactor (2) code style (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 20 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
pypi.org: arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 20 Last month
Rankings
Dependent packages count: 9.5%
Average: 36.1%
Dependent repos count: 62.7%
Maintainers (1)
bonvinlab
Last synced: 6 months ago

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v3 composite
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  • codacy/codacy-coverage-reporter-action v1 composite
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poetry.lock pypi
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  • idna 3.4
  • joblib 1.2.0
  • jsonpickle 3.0.1
  • kiwisolver 1.4.4
  • lxml 4.9.2
  • matplotlib 3.6.3
  • mdanalysis 2.4.2
  • mmtf-python 1.1.3
  • mrcfile 1.4.3
  • msgpack 1.0.4
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  • pillow 9.4.0
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  • pyparsing 3.0.9
  • python-dateutil 2.8.2
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  • tenacity 8.1.0
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pyproject.toml pypi
  • bio 1.5.3
  • biopython 1.80
  • defusedxml 0.7.1
  • jsonpickle 3.0.1
  • lxml 4.9.2
  • matplotlib 3.6.3
  • mdanalysis 2.4.2
  • openpyxl 3.0.10
  • pandas 1.5.3
  • pdb-tools 2.5.0
  • pdbecif 1.5
  • plotly 5.13.0
  • python >=3.9,<3.12
  • requests 2.28.2
  • scipy 1.10.0