{"id":45454625,"url":"https://github.com/kavrakilab/ape-gen2.0","last_synced_at":"2026-02-22T06:03:16.436Z","repository":{"id":224745455,"uuid":"449818404","full_name":"KavrakiLab/Ape-Gen2.0","owner":"KavrakiLab","description":null,"archived":false,"fork":false,"pushed_at":"2025-07-10T15:28:18.000Z","size":412068,"stargazers_count":3,"open_issues_count":5,"forks_count":3,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-10T21:57:00.581Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KavrakiLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2022-01-19T18:57:38.000Z","updated_at":"2025-07-10T15:28:29.000Z","dependencies_parsed_at":"2025-07-10T17:44:18.613Z","dependency_job_id":null,"html_url":"https://github.com/KavrakiLab/Ape-Gen2.0","commit_stats":null,"previous_names":["kavrakilab/ape-gen2.0"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/KavrakiLab/Ape-Gen2.0","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KavrakiLab%2FApe-Gen2.0","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KavrakiLab%2FApe-Gen2.0/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KavrakiLab%2FApe-Gen2.0/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KavrakiLab%2FApe-Gen2.0/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KavrakiLab","download_url":"https://codeload.github.com/KavrakiLab/Ape-Gen2.0/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KavrakiLab%2FApe-Gen2.0/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29705846,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-22T05:59:28.568Z","status":"ssl_error","status_checked_at":"2026-02-22T05:58:46.208Z","response_time":110,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":[],"created_at":"2026-02-22T06:03:15.567Z","updated_at":"2026-02-22T06:03:16.430Z","avatar_url":"https://github.com/KavrakiLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# New Ape-Gen version:\n\n## Prelims\n\nTo set up APE-Gen2.0 locally, download the repo using `git clone`.\n\nBefore you move on to anything else, am important step must be performed: Download the frequency matrices generated using MHCFlurry2.0 through the link below:\n\nhttps://rice.box.com/s/duxshqxtkykg7u9y3b0tl79j8byc2dp2\n\nThese will be crucial for the softawre to run. After these are downloaded, go ahead and put those on the `helper_files` folder. Then you're all set for the installation!\n\n## Installation\n\nWe recommend that APE-Gen2.0 is set up with a docker configuration, so the latest version of `docker` should be installed on your system. Setting APE-Gen2.0 through a python virtual env is definitely plausible (check the `environment.yml`and the provided `Dockerfile` for all needed packages), but we'll leave that to you if you want to set it up this way. \n\nJust running:\n```\nbash build_image.sh\n```\n\nshould build the docker image After this, just running:\n```\nbash start_image.sh\n```\n\ngets you into the container, APE-Gen2.0 can be run from there. \n\n## Usage\n\nTo run APE-Gen2.0 for existing MHC templates in the database, you should be good to go (Ignore the warning message about the MODELLER invalid key). However, for a new MHC not found in the database, you will need to provide a valid MODELLER key. To do that, go to:\n\n```\ncd /conda/envs/apegen/lib/modeller-10.4/modlib/modeller/\n```\n\nand modify the lines of `config.py` with a valid MODELLER key.\n\nFor now, peptide sequence (along with positions with PTM) + an MHC allotype should work! (more inputs to follow...)\n\n```\npython New_APE-Gen.py LLGIGSLTV HLA-A*02:01 --verbose\npython New_APE-Gen.py LLGIGSLTV HLA-A*02:01 --verbose --score_with_openmm\npython New_APE-Gen.py LLGIGpSLTV HLA-A*02:01 --verbose --score_with_openmm\npython New_APE-Gen.py LLGpSGpSLTV HLA-A*02:01 --verbose --score_with_openmm\n```\n\nPlease contact the team should you have any issues with running APE-Gen2.0!\n\n## Citation\n\n```\n@article{Fasoulis2024,\n  title = {APE-Gen2.0: Expanding Rapid Class I Peptide–Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries},\n  volume = {64},\n  ISSN = {1549-960X},\n  url = {http://dx.doi.org/10.1021/acs.jcim.3c01667},\n  DOI = {10.1021/acs.jcim.3c01667},\n  number = {5},\n  journal = {Journal of Chemical Information and Modeling},\n  publisher = {American Chemical Society (ACS)},\n  author = {Fasoulis,  Romanos and Rigo,  Mauricio M. and Lizée,  Gregory and Antunes,  Dinler A. and Kavraki,  Lydia E.},\n  year = {2024},\n  month = feb,\n  pages = {1730–1750}\n}\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkavrakilab%2Fape-gen2.0","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkavrakilab%2Fape-gen2.0","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkavrakilab%2Fape-gen2.0/lists"}