{"id":44964492,"url":"https://github.com/bioinfomachinelearning/gd-multimer","last_synced_at":"2026-02-18T14:09:40.551Z","repository":{"id":104968771,"uuid":"501876552","full_name":"BioinfoMachineLearning/GD-multimer","owner":"BioinfoMachineLearning","description":"Stochastic gradient descent method for reconstructing protein multimer structures from inter-chain 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returned=1 errno=0 peeraddr=140.82.121.5:443 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":"2026-02-18T14:09:39.743Z","updated_at":"2026-02-18T14:09:40.546Z","avatar_url":"https://github.com/BioinfoMachineLearning.png","language":"Python","readme":"# GD-multimer\nStochastic gradient descent method for reconstructing protein multimer structures from inter-chain contacts/distances\n\n\n\n** Download GD-Multimer package (short path is recommended)**\n\n```\ngit clone git@github.com:BioinfoMachineLearning/GD-multimer.git\n\n(If fail, try username) git clone https://github.com/BioinfoMachineLearning/GD-multimer.git\n\ncd GFOLD\n```\n\n** How to run the code:**\n\n```\nFor dimers using contact:\n\npython ./scripts/docking_new.py target_name first_chain second_chain res_file output_dir weight_file top_num\n\nexample:\n\npython ./scripts/docking_new.py T0965A_T0965B GD_tools/pdb_homo/chains/T0965A.pdb GD_tools/pdb_homo/chains/T0965B.pdb ../output_distance/T0965A_T0965B_con.rr ./ ./talaris2013.wts all\n```\n\n```\nFor dimers using distance:\n\npython ./scripts/docking_new_dist.py target_name first_chain second_chain res_file output_dir weight_file thre \n\nexample:\n\npython ./scripts/docking_new_dist.py T0965A_T0965B GD_tools/pdb_homo/chains/T0965A.pdb GD_tools/pdb_homo/chains/T0965B.pdb ../output_distance/T0965A_T0965B_dist.rr ./ ./talaris2013.wts 6\n```\n\n```\nFor multimers using contact:\n\n\npython ./scripts/docking_gd_parallel_multi.py target_name num_of_chains first_chain second_chain third_chain ... nth_chain res_file output_dir weight_file top_num\n\n\nexample:\n\npython ./scripts/docking_gd_parallel_multi.py T1034 4 /home/esdft/Downloads/pdbs/initial_start_multi/T1034A.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034B.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034C.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034D.pdb /home/esdft/Downloads/output_distance/T1034o.rr /home/esdft/Downloads/pdbs/ ./talaris2013.wts all\n```\n\n```\nFor multimers using distance:\n\n\npython ./scripts/docking_gd_parallel_multi_dist.py target_name num_of_chains first_chain second_chain third_chain ... nth_chain res_file output_dir weight_file thre\n\n\nexample:\n\npython ./scripts/docking_gd_parallel_multi_dist.py T1034 4 /home/esdft/Downloads/pdbs/initial_start_multi/T1034A.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034B.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034C.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034D.pdb /home/esdft/Downloads/output_distance/T1034o.rr /home/esdft/Downloads/pdbs/ ./talaris2013.wts 36\n```\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioinfomachinelearning%2Fgd-multimer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioinfomachinelearning%2Fgd-multimer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioinfomachinelearning%2Fgd-multimer/lists"}