{"id":30893221,"url":"https://github.com/rosettacommons/modelforge","last_synced_at":"2025-09-08T20:06:09.588Z","repository":{"id":310107293,"uuid":"1037755418","full_name":"RosettaCommons/modelforge","owner":"RosettaCommons","description":"Central repository for biomolecular foundation models with shared trainers and pipeline components","archived":false,"fork":false,"pushed_at":"2025-08-29T14:02:20.000Z","size":51928,"stargazers_count":118,"open_issues_count":5,"forks_count":10,"subscribers_count":4,"default_branch":"production","last_synced_at":"2025-08-29T16:56:22.650Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/RosettaCommons.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"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":"2025-08-14T04:31:40.000Z","updated_at":"2025-08-29T14:02:25.000Z","dependencies_parsed_at":null,"dependency_job_id":"0f22fa70-98cd-432c-ba16-bb18c3201ac0","html_url":"https://github.com/RosettaCommons/modelforge","commit_stats":null,"previous_names":["rosettacommons/modelforge"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/RosettaCommons/modelforge","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RosettaCommons%2Fmodelforge","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RosettaCommons%2Fmodelforge/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RosettaCommons%2Fmodelforge/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RosettaCommons%2Fmodelforge/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/RosettaCommons","download_url":"https://codeload.github.com/RosettaCommons/modelforge/tar.gz/refs/heads/production","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RosettaCommons%2Fmodelforge/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274231512,"owners_count":25245600,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-08T02:00:09.813Z","response_time":121,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2025-09-08T20:06:07.721Z","updated_at":"2025-09-08T20:06:09.574Z","avatar_url":"https://github.com/RosettaCommons.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Open-Source Neural Networks for Biomolecular Tasks\n\n`ModelForge` is a repository of open-source models for common biomolecular tasks, including structure prediction, fixed-backbone sequence design (\"inverse folding\"), and *de novo* protein design.\n\nAll models within `ModelForge` share a common training harness and integrate with [AtomWorks](https://github.com/RosettaCommons/atomworks) – our generalized computational framework for biomolecular modeling.\n\nFor more information, please see our preprint, [Accelerating Biomolecular Modeling with AtomWorks and RF3](https://doi.org/10.1101/2025.08.14.670328).\n\n\u003e **⚠️ Notice:** We fixed an inference bug on 8/29 that arose during codebase migration and impacted predictions from JSON and from mmCIF/PDB; the issue is now resolved but for the purposes of model benchmarking predictions should be re-run.\n\n\u003e **⚠️ Notice:** We are currently finalizing some cleanup work within our repositories. Please expect the APIs (e.g., function and class names, inputs and outputs) to stabilize within the next two weeks. Thank you for your patience!\n\n\u003e **⚠️ Notice:** Training code coming very soon, with documentation on how to fine-tune on new datasets! \n\n## Supported Networks\n\n### RosettaFold3 (RF3)\n\n[RF3](https://doi.org/10.1101/2025.08.14.670328) is a structure prediction neural network that narrows the gap between closed-source AF-3 and open-source alternatives.\n\n\u003cdiv align=\"center\"\u003e\n  \u003cimg src=\"docs/_static/prot_dna.png\" alt=\"Protein-DNA complex prediction\" width=\"400\"\u003e\n\u003c/div\u003e\n\nComplete inference instructions for RF3 are provided [here](src/modelhub/inference_engines/README.md).\n\n## Installation \u0026 Usage\n\nFollow these steps to set up **ModelForge** and run a test prediction.\n\n---\n\n### 1. Install the repository using `uv`\n\n```bash\ngit clone https://github.com/RosettaCommons/modelforge.git \\\n  \u0026\u0026 cd modelforge \\\n  \u0026\u0026 uv python install 3.12 \\\n  \u0026\u0026 uv venv --python 3.12 \\\n  \u0026\u0026 source .venv/bin/activate \\\n  \u0026\u0026 uv pip install -e .\n```\n\n### 2. Download model weights for RF3 \n```bash\nwget http://files.ipd.uw.edu/pub/rf3/rf3_latest.pt\n```\n\n### 3. Run a test prediction\n```bash\nrf3 fold tests/data/5vht_from_json.json\n```\n\nDetails on the exact formatting of the json files are available [here](src/modelhub/inference_engines/README.md).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frosettacommons%2Fmodelforge","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frosettacommons%2Fmodelforge","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frosettacommons%2Fmodelforge/lists"}