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Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Models Challenge hosted at challenges.emdatabank.org are deposited.
\n\nAll members of the Scientific Community--at all levels of experience--were invited to participate as Challengers, and/or as Assessors.
\n\nEight recently determined target structures were selected for the challenge. All of the maps were archived in the EM Data Bank (EMDB; http://emdatabank.org).
\n\nIn total 16 Challengers created 106 models and uploaded their results with associated details. In the zip files, each entry is represented in a folder containing the original deposition upload (deposited_EM.pdb), initial processing at RCSB/Rutgers (deposited_EM_edited.pdb, maxit.cif, maxit.cif.pdb) and final model version evaluated (model-compare.pdb) at UC Davis (http://model-compare.emdatabank.org).
\n\nThis model challenge was one of two community-wide challenges sponsored by EMDataBank in 2015/2016 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model.
\n\n", "languages": [ { "id": "eng", "title": { "en": "English" } } ], "publication_date": "2018-01-24", "publisher": "Zenodo", "references": [ { "reference": "Henderson et al (2012) Outcome of the first electron microscopy validation task force meeting. doi:10.1016/j.str.2011.12.014" }, { "reference": "Lawson et al (2016) EMDataBank unified data resource for 3DEM. doi:10.1093/nar/gkv1126" } ], "related_identifiers": [ { "identifier": "10.1093/nar/gkv1126", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "doi" }, { "identifier": "http://challenges.emdatabank.org", "relation_type": { "id": "documents", "title": { "de": "Dokumentiert", "en": "Documents" } }, "scheme": "url" }, { "identifier": "10.1016/j.jsb.2016.02.008", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "doi" }, { "identifier": "http://model-compare.emdatabank.org", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "url" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited." }, "icon": "cc-by-icon", "id": "cc-by-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution 4.0 International" } } ], "subjects": [ { "subject": "cryo electron microscopy" }, { "subject": "cryoEM" }, { "subject": "validation" }, { "subject": "challenge" }, { "subject": "benchmark" } ], "title": "CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge", "version": "1.1" }, "parent": { "access": { "owned_by": { "user": 38522 } }, "communities": { "default": "8f2e2407-d10a-46dd-9e26-59b84ddd3574", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2017-12-20T16:59:52.508060+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "8f2e2407-d10a-46dd-9e26-59b84ddd3574", "links": {}, "metadata": { "curation_policy": "
This community collection is intended for archiving the data from validation challenges hosted by the Unified Data Resource for 3DEM (emdataresource.org) Datasets related to cryoEM validation and standards development generated by other resources are also welcome.
\r\n", "description": "Structures (Maps, Models) and associated Metadata for 3D Cryo Electron Microscopy (CryoEM) Community Validation Challenges", "page": "Three-dimensional Electron Microscopy (3DEM) is becoming a key experimental method in Structural Biology. Recent advances in image acquisition and processing are yielding more structures determined at near-atomic resolution, as well as a wide range of macromolecular complexes and subcellular architectures determined at lower resolution.
\r\n\r\nA major goal of the Unified Data Resource for 3DEM team is to work with the 3DEM community to establish data validation methods that can be used in the structure determination process, define key indicators of a well-determined structure that should accompany every structure deposition, and implement appropriate validation procedures into a 3DEM validation pipeline. Following recommendations of the EM Validation Task Force (Henderson et al 2012), we are hosting new benchmark challenges, with aim to stimulate further community discussions about validation procedures for 3DEM maps and map-derived models. Prior community-organized 3DEM challenge activities have included a Particle Picking Challenge (Zhu et al 2004), CryoEM Modeling Challenge (Ludtke et al 2012), and CTF Challenge (Marabini et al 2015).
\r\n", "title": "3D Cryo Electron Microscopy Community Challenges" }, "revision_id": 0, "slug": "3dcryoemchallenges", "updated": "2020-10-28T21:24:30.427595+00:00" } ], "ids": [ "8f2e2407-d10a-46dd-9e26-59b84ddd3574" ] }, "id": "1137818", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.1137818", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.1165999", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:1165999", "provider": "oai" } }, "revision_id": 8, "stats": { "all_versions": { "data_volume": 71596850215.0, "downloads": 355, "unique_downloads": 236, "unique_views": 653, "views": 681 }, "this_version": { "data_volume": 62677131358.0, "downloads": 303, "unique_downloads": 210, "unique_views": 405, "views": 430 } }, "status": "published", "updated": "2020-01-24T19:24:50.383031+00:00", "versions": { "index": 2, "is_latest": true } }