{"id":40685668,"url":"https://github.com/haddocking/arctic3d","last_synced_at":"2026-01-21T10:43:37.067Z","repository":{"id":61182563,"uuid":"509065982","full_name":"haddocking/arctic3d","owner":"haddocking","description":"Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information","archived":false,"fork":false,"pushed_at":"2025-12-03T15:05:11.000Z","size":2084,"stargazers_count":32,"open_issues_count":2,"forks_count":6,"subscribers_count":12,"default_branch":"main","last_synced_at":"2025-12-06T19:49:44.368Z","etag":null,"topics":["clustering","data-mining","data-retrieval","macromolecular-modeling","pdbe-s-rest-api","protein-docking","utrecht-university"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/haddocking.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-06-30T12:12:44.000Z","updated_at":"2025-12-03T15:05:14.000Z","dependencies_parsed_at":"2023-10-04T15:38:00.348Z","dependency_job_id":"cc108efc-4959-48d4-b3ab-2db78f40b937","html_url":"https://github.com/haddocking/arctic3d","commit_stats":null,"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/haddocking/arctic3d","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haddocking%2Farctic3d","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haddocking%2Farctic3d/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haddocking%2Farctic3d/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haddocking%2Farctic3d/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/haddocking","download_url":"https://codeload.github.com/haddocking/arctic3d/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haddocking%2Farctic3d/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28631957,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-21T04:47:28.174Z","status":"ssl_error","status_checked_at":"2026-01-21T04:47:22.943Z","response_time":86,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["clustering","data-mining","data-retrieval","macromolecular-modeling","pdbe-s-rest-api","protein-docking","utrecht-university"],"created_at":"2026-01-21T10:43:36.166Z","updated_at":"2026-01-21T10:43:37.060Z","avatar_url":"https://github.com/haddocking.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ARCTIC-3D\n\n![PyPI - License](https://img.shields.io/pypi/l/arctic3d)\n![PyPI - Status](https://img.shields.io/pypi/status/arctic3d)\n![PyPI - Version](https://img.shields.io/pypi/v/arctic3d)\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/arctic3d)\n\n[![ci](https://github.com/haddocking/arctic3d/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/arctic3d/actions/workflows/ci.yml)\n[![Codacy Badge](https://app.codacy.com/project/badge/Coverage/dc788367452c47928e30f2f1f481d7e4)](https://www.codacy.com/gh/haddocking/arctic3d/dashboard?utm_source=github.com\u0026utm_medium=referral\u0026utm_content=haddocking/arctic3d\u0026utm_campaign=Badge_Coverage)\n[![Codacy Badge](https://app.codacy.com/project/badge/Grade/dc788367452c47928e30f2f1f481d7e4)](https://www.codacy.com/gh/haddocking/arctic3d/dashboard?utm_source=github.com\u0026utm_medium=referral\u0026utm_content=haddocking/arctic3d\u0026utm_campaign=Badge_Grade)\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10839520.svg)](https://doi.org/10.5281/zenodo.10839520)\n[![SQAaaS badge shields.io](https://img.shields.io/badge/sqaaas%20software-bronze-e6ae77)](https://api.eu.badgr.io/public/assertions/oAuS52pQTWaC90qMk97hlA \"SQAaaS bronze badge achieved\")\n[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)\n\n\n[![SQAaaS badge](https://github.com/EOSC-synergy/SQAaaS/raw/master/badges/badges_150x116/badge_software_bronze.png)](https://api.eu.badgr.io/public/assertions/oAuS52pQTWaC90qMk97hlA \"SQAaaS bronze badge achieved\")\n\n\u003cimg src=\"https://raw.githubusercontent.com/haddocking/arctic3d/main/docs/imgs/arctic3d.png\" width=\"450\"\u003e\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, 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)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaddocking%2Farctic3d","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhaddocking%2Farctic3d","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaddocking%2Farctic3d/lists"}