{"id":13685281,"url":"https://github.com/flatironinstitute/deepblast","last_synced_at":"2025-07-10T16:35:11.286Z","repository":{"id":39109639,"uuid":"269478463","full_name":"flatironinstitute/deepblast","owner":"flatironinstitute","description":"Neural Networks for Protein Sequence Alignment","archived":false,"fork":false,"pushed_at":"2024-11-11T18:12:13.000Z","size":59480,"stargazers_count":121,"open_issues_count":34,"forks_count":22,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-05-18T03:07:11.246Z","etag":null,"topics":["language-modeling","neural-networks","protein","protein-sequences","protein-structure","sequence-alignment","structural-alignments"],"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/flatironinstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING.txt","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}},"created_at":"2020-06-04T22:28:59.000Z","updated_at":"2025-05-08T12:10:36.000Z","dependencies_parsed_at":"2024-11-11T19:32:00.075Z","dependency_job_id":null,"html_url":"https://github.com/flatironinstitute/deepblast","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/flatironinstitute/deepblast","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Fdeepblast","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Fdeepblast/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Fdeepblast/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Fdeepblast/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/flatironinstitute","download_url":"https://codeload.github.com/flatironinstitute/deepblast/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Fdeepblast/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264608242,"owners_count":23636690,"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","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":["language-modeling","neural-networks","protein","protein-sequences","protein-structure","sequence-alignment","structural-alignments"],"created_at":"2024-08-02T14:00:48.129Z","updated_at":"2025-07-10T16:35:06.272Z","avatar_url":"https://github.com/flatironinstitute.png","language":"Python","funding_links":[],"categories":["Sequence similarity search and (structural) alignment"],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/269478463.svg)](https://zenodo.org/badge/latestdoi/269478463)\n\n\n# DeepBLAST \n\nLearning protein structural similarity from sequence alone.  Our preprint can be found [here](https://www.biorxiv.org/content/10.1101/2020.11.03.365932v1)\n\nDeepBLAST is a neural-network based alignment algorithm that can estimate structural alignments. And it can generate structural alignments that are nearly identical to\nstate-of-the-art structural alignment algorithms.\n![Malidup benchmark](/imgs/malidup.png)\n\n# Installation\n\nDeepBLAST can be installed from pip via\n\n```\npip install deepblast\n```\n\nTo install from the development branch run\n\n```\npip install git+https://github.com/flatironinstitute/deepblast.git\n```\n\n# Downloading pretrained models and data\n\n- [DeepBLAST and TMvec checkpoints](https://figshare.com/articles/dataset/TMvec_DeepBLAST_models/25810099)\n- [Training data and databases](https://zenodo.org/records/11199459)\n\n\nSee the [Malisam](http://prodata.swmed.edu/malisam/) and [Malidup](http://prodata.swmed.edu/malidup/) websites to download their datasets.\n\n# Getting started\n\nSee the [wiki](https://github.com/flatironinstitute/deepblast/wiki) on how to use DeepBLAST and TM-vec for remote homology search and alignment.\nIf you have questions on how to use DeepBLAST and TM-vec, feel free to raise questions in the [discussions section](https://github.com/flatironinstitute/deepblast/discussions). If you identify any potential bugs, feel free to raise them in the [issuetracker](https://github.com/flatironinstitute/deepblast/issues)\n\n# Citation\n\nIf you find our work useful, please cite us at\n```\n@article{morton2020protein,\n  title={Protein Structural Alignments From Sequence},\n  author={Morton, Jamie and Strauss, Charlie and Blackwell, Robert and Berenberg, Daniel and Gligorijevic, Vladimir and Bonneau, Richard},\n  journal={bioRxiv},\n  year={2020},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n@article{hamamsy2022tm,\n  title={TM-Vec: template modeling vectors for fast homology detection and alignment},\n  author={Hamamsy, Tymor and Morton, James T and Berenberg, Daniel and Carriero, Nicholas and Gligorijevic, Vladimir and Blackwell, Robert and Strauss, Charlie EM and Leman, Julia Koehler and Cho, Kyunghyun and Bonneau, Richard},\n  journal={bioRxiv},\n  pages={2022--07},\n  year={2022},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fflatironinstitute%2Fdeepblast","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fflatironinstitute%2Fdeepblast","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fflatironinstitute%2Fdeepblast/lists"}