{"id":26753152,"url":"https://github.com/d-f/binding-affinity","last_synced_at":"2026-05-03T06:41:35.951Z","repository":{"id":283529731,"uuid":"952074909","full_name":"d-f/binding-affinity","owner":"d-f","description":"Protein-Ligand binding affinity prediction with Protein LLMs and Graph Attention Networks.","archived":false,"fork":false,"pushed_at":"2025-04-27T22:50:16.000Z","size":25,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-27T23:24:44.648Z","etag":null,"topics":["binding-affinity","binding-affinity-prediction","graph-attention-networks","pdb-dataset","protein-llm","pytorch"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/d-f.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2025-03-20T17:33:38.000Z","updated_at":"2025-03-20T20:12:30.000Z","dependencies_parsed_at":"2025-04-27T23:22:03.777Z","dependency_job_id":"994d73f7-f59d-4913-ba95-34bb288520ea","html_url":"https://github.com/d-f/binding-affinity","commit_stats":null,"previous_names":["d-f/binding-affinity"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/d-f/binding-affinity","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/d-f%2Fbinding-affinity","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/d-f%2Fbinding-affinity/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/d-f%2Fbinding-affinity/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/d-f%2Fbinding-affinity/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/d-f","download_url":"https://codeload.github.com/d-f/binding-affinity/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/d-f%2Fbinding-affinity/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32560914,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-03T06:36:36.687Z","status":"ssl_error","status_checked_at":"2026-05-03T06:36:09.306Z","response_time":103,"last_error":"SSL_read: 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":["binding-affinity","binding-affinity-prediction","graph-attention-networks","pdb-dataset","protein-llm","pytorch"],"created_at":"2025-03-28T13:17:59.566Z","updated_at":"2026-05-03T06:41:35.940Z","avatar_url":"https://github.com/d-f.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"To determine the mean and standard deviation of dataset features:\n```\npython determine_affinity_stats.py -save_filepath /affinity/ds_stats.json\n```\n\nTo partition the dataset into training, validation and test partitions:\n```\npython partition_dataset.py -data_folder /affinity/processed/ -save_folder /affinity/\n```\n\nTo embed the dataset proteins with ProtBERT and dataset ligands with ChemBERTa:\n```\npython process_plapt_ds.py -stat_json_path /affinity/ds_stats.json -save_dir /affinity/processed/\n```\n\nTo train a PLAPT model to predict binding affinity:\n```\npython train_plapt.py -data_folder /affinity/processed/ -csv_folder /affinity/csv/ -batch_size 64 -lr 1e-3 -num_epochs 64 -result_folder /affinity/models/ -model_save_name model_1.pth.tar -patience 5 -prot_hidden 512 -lig_hidden 512\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fd-f%2Fbinding-affinity","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fd-f%2Fbinding-affinity","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fd-f%2Fbinding-affinity/lists"}