{"id":17255107,"url":"https://github.com/unixjunkie/consent","last_synced_at":"2025-10-06T14:33:37.449Z","repository":{"id":144782294,"uuid":"81097256","full_name":"UnixJunkie/consent","owner":"UnixJunkie","description":"ligand-based virtual screening with consensus queries","archived":false,"fork":false,"pushed_at":"2023-10-27T14:14:39.000Z","size":147,"stargazers_count":8,"open_issues_count":1,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-27T19:23:06.375Z","etag":null,"topics":["chemical","chemoinformatics","consensus","ecfp4","fingerprint","lbvs","ligand","maccs","molprint2d","ocaml"],"latest_commit_sha":null,"homepage":"","language":"OCaml","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":"2017-02-06T14:47:31.000Z","updated_at":"2023-12-14T09:39:14.000Z","dependencies_parsed_at":"2024-10-15T07:10:48.510Z","dependency_job_id":"178dff5a-ea55-489a-964d-6841c2d5630c","html_url":"https://github.com/UnixJunkie/consent","commit_stats":{"total_commits":96,"total_committers":3,"mean_commits":32.0,"dds":0.5,"last_synced_commit":"eeb2824b512f79b30a84377df2a1c017a7e46e46"},"previous_names":[],"tags_count":15,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Fconsent","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Fconsent/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Fconsent/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Fconsent/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/consent/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248830416,"owners_count":21168271,"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":["chemical","chemoinformatics","consensus","ecfp4","fingerprint","lbvs","ligand","maccs","molprint2d","ocaml"],"created_at":"2024-10-15T07:10:43.225Z","updated_at":"2025-10-06T14:33:32.424Z","avatar_url":"https://github.com/UnixJunkie.png","language":"OCaml","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Consent\nChemoinformatics software for Ligand-Based Virtual Screening (LBVS)\nusing consensus queries.\n\nCf. the INSTALL file for instructions on how to install consent.\n\n# I) Command line help\n\n    lbvs_consent -s {sing|oppo|opti|real|know}\n                 -q queries.{sdf|mol2|csv|ecfp4}\n                 -db candidates.{sdf|mol2|csv|ecfp4}\n\n      -s \u003cpol\u003e consensus policy {sing|oppo|opti|real|know} (mandatory)\n      -q \u003cfilename\u003e queries file (known actives; mandatory)\n      -db \u003cfilename\u003e database to rank order (mandatory)\n      -o \u003cfilename\u003e where to write scores (can be combined with -top)\n      -n \u003cint\u003e consensus size; #known actives used to create query (optional;\n               default=all molecules in query file)\n      -top \u003cint\u003e how many top scoring molecules to write out (optional;\n           default=all; must be combined with -o)\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1006728.svg)](https://doi.org/10.5281/zenodo.1006728)\n\n# II) Usage recommendation\n\nPlease cite the corresponding paper (https://doi.org/10.1186/s13321-017-0248-5)\nin case you use this software and publish about your results\n(Consensus queries in ligand-based virtual screening experiments.\nF. Berenger, O. Vu and J., Meiler. Journal of Cheminformatics, November 2017).\n\nThe opportunist consensus policy (-s oppo) is recommended.\nIt works well with any fingerprint and is usually the best performing\nmethod.\n\nHowever, if you really need to go faster, here are some recommendations:\n\n- MACCS fingerprint (166 bits): use the realistic policy (-s real); it will\n  average the MACCS fingerprints of your known actives.\n\n- ECFP4 fingerprint (2048 bits; folded; uncounted):\n  use the optimist policy (-s opti); it will\n  do a logical union of the fingerprints of your known actives.\n\n- UMOP2D (unfolded MOLPRINT2D; uncounted): same as for ECFP4, use -s opti.\n\n# III) How to encode your molecules\n\nFirst, we need some SDF and MOL2 files.\nThe obabel command is provided by the Open Babel package\n(cf. http://openbabel.org).\n\n    obabel data/ARm_actives.smi -O data/ARm_actives.sdf\n    obabel data/ARm_inactives.smi -O data/ARm_inactives.sdf\n    obabel data/ARm_actives.smi -O data/ARm_actives.mol2\n    obabel data/ARm_inactives.smi -O data/ARm_inactives.mol2\n    cat data/ARm_actives.mol2 data/ARm_inactives.mol2 \u003e data/ARm_database.mol2\n\n## With the MACCS fingerprint\n\n    lbvs_consent_ob_maccs data/ARm_actives.sdf \u003e data/ARm_actives.maccs\n    lbvs_consent_ob_maccs data/ARm_inactives.sdf \u003e data/ARm_inactives.maccs\n    cat data/ARm_actives.maccs data/ARm_inactives.maccs \u003e data/ARm_database.maccs\n\n## With the ECFP4 fingerprint\n\n    lbvs_consent_ecfp4.py data/ARm_actives.sdf \u003e data/ARm_actives.ecfp4\n    lbvs_consent_ecfp4.py data/ARm_inactives.sdf \u003e data/ARm_inactives.ecfp4\n    cat data/ARm_actives.ecfp4 data/ARm_inactives.ecfp4 \u003e data/ARm_database.ecfp4\n\n## With the UMOP2D fingerprint\n\n    lbvs_consent_mop2di -i data/ARm_database.mol2 \u003e data/ARm_database.idx\n    lbvs_consent_mop2de -idx data/ARm_database.idx -i data/ARm_database.mol2 -o data/ARm_database.mop2d\n\n# IV) How to query with a consensus query and a consensus policy\n\n    # example with ECFP4 fingerprints and 20 actives\n    head -20 data/ARm_actives.ecfp4 \u003e data/ARm_query_20.ecfp4\n    # recommended way; AUC ~= 0.60\n    lbvs_consent -s oppo -q data/ARm_query_20.ecfp4 -db data/ARm_database.ecfp4 -o scores.txt\n    # faster, but still with good performance in many cases; AUC ~= 0.61\n    lbvs_consent -s opti -q data/ARm_query_20.ecfp4 -db data/ARm_database.ecfp4 -o scores.txt\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fconsent","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fconsent","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fconsent/lists"}