{"id":26753152,"url":"https://github.com/d-f/binding-affinity","last_synced_at":"2025-03-28T13:18:00.255Z","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":"2025-03-20T17:43:54.000Z","size":10,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-20T18:34:48.602Z","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}},"created_at":"2025-03-20T17:33:38.000Z","updated_at":"2025-03-20T17:43:58.000Z","dependencies_parsed_at":"2025-03-20T18:51:27.746Z","dependency_job_id":null,"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,"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","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246034312,"owners_count":20712857,"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":["binding-affinity","binding-affinity-prediction","graph-attention-networks","pdb-dataset","protein-llm","pytorch"],"created_at":"2025-03-28T13:17:59.566Z","updated_at":"2025-03-28T13:18:00.252Z","avatar_url":"https://github.com/d-f.png","language":"Python","readme":"```process_dataset.py``` processes the PDBBind dataset through the deepchem library. It will embed the sequence of amino acid abbreviations with a Protein LLM, convert the rdkit Molecule objects into torch_geometric graphs and saves the binding affinity each in separate directories. \n\n```determine_bond_types.py``` determines which bond types are present within the dataset for nomalization purposes\n\n```train_models.py``` allows for training a pure GAT or a combination of a GAT and Transformer depending on what is set for the model_type parameter. If a pure GAT is used, protein LLM embeddings are concatenated to atomic features when creating a ligand molecule graph and the graph is used for whole graph regression. If a combination of transformer and GAT is used, the GAT will be used to embed the graph, and a transformer will predict the binding affinity between the protein embedding and embedded ligand graph.\n","funding_links":[],"categories":[],"sub_categories":[],"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"}