{"id":17255142,"url":"https://github.com/unixjunkie/seed","last_synced_at":"2025-03-26T08:16:02.596Z","repository":{"id":144782701,"uuid":"290380956","full_name":"UnixJunkie/SEED","owner":"UnixJunkie","description":"mirror of https://gitlab.com/CaflischLab/SEED.git","archived":false,"fork":false,"pushed_at":"2020-08-26T03:04:16.000Z","size":19478,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-31T09:31:14.398Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/UnixJunkie.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}},"created_at":"2020-08-26T03:03:28.000Z","updated_at":"2023-11-21T09:31:33.000Z","dependencies_parsed_at":null,"dependency_job_id":"c8d643e7-512e-49ea-8bbb-e46d9348e461","html_url":"https://github.com/UnixJunkie/SEED","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FSEED","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FSEED/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FSEED/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FSEED/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/SEED/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245615009,"owners_count":20644376,"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":[],"created_at":"2024-10-15T07:10:48.145Z","updated_at":"2025-03-26T08:16:02.577Z","avatar_url":"https://github.com/UnixJunkie.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SEED (Solvation Energy for Exhaustive Docking) version 4.0.0\n\nSEED is a program for fragment docking with force-field based evaluation of binding energy.\n\nThe new SEED documentation is now online at: [https://caflischlab-seed.readthedocs.io/en/latest/](https://caflischlab-seed.readthedocs.io/en/latest/)!\n\nFor details about the energy models implemented in SEED please refer to the original publications and to the pdf user manual (seed_4.0.0_doc.pdf).\n\n### Installation ###\ncd to directory src and make SEED with the following command (you may have to modify the Makefile.local):\n```sh\nmake seed\n```\nThe binary is compiled into the bin directory.\n### Run SEED ###\nRun SEED with the following command:\n```sh\n./seed_4 seed.inp \u003e\u0026 log\n```\nYou can find an example seed.inp and seed.par, along with the results of simple study cases,\nin the test_cases folder.\n\n### Citations ###\nReview of the applications of SEED in the period 1999-2018, includes a discussion on its strenghts/weaknesses in light of our experience:\n * J.-R. Marchand, and A. Caflisch. In silico fragment-based drug design with SEED.\nEuropean Journal of Medicinal Chemistry, 156:907-917, 2018.\n\nOriginal paper describing SEED:\n * N. Majeux, M. Scarsi, J. Apostolakis, C. Ehrhardt, and A. Caflisch. Exhaustive docking of\nmolecular fragments on protein binding sites with electrostatic solvation.\nProteins: Structure, Function and Genetics, 37:88-105, 1999.\n\nThe description of the fast energy evaluation is in the second SEED paper:\n * N. Majeux, M. Scarsi, and A. Caflisch. Efficient electrostatic solvation model for protein-\nfragment docking.\nProteins: Structure, Function and Genetics, 42:256-268, 2001.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fseed","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fseed","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fseed/lists"}