{ "access": { "embargo": { "active": false, "reason": null }, "files": "public", "record": "public", "status": "open" }, "created": "2018-04-13T17:44:12.910521+00:00", "custom_fields": { "journal:journal": { "pages": "2927-43", "title": "Mol Cell Proteomics", "volume": "13" } }, "deletion_status": { "is_deleted": false, "status": "P" }, "files": { "count": 9, "enabled": true, "entries": { "Fig_6_densities.zip": { "checksum": "md5:5671e1b81162c022cac9736f0b6c8062", "ext": "zip", "id": "ca5fc79e-6bff-4b5b-a338-a0559e23931e", "key": "Fig_6_densities.zip", "metadata": null, "mimetype": "application/zip", "size": 83738427 }, "XL_analysis.zip": { "checksum": "md5:95f62167280853f183b4c5da55c84111", "ext": "zip", "id": "29d305c0-2c6a-41e4-b08b-164192f7b405", "key": "XL_analysis.zip", "metadata": null, "mimetype": "application/zip", "size": 5149246 }, "clus.1.aligned.dcd": { "checksum": "md5:db3d8b3272b8297b7d95bd1932a474b6", "ext": "dcd", "id": "77452ea5-3d1e-4d4b-9b93-4249f9074524", "key": "clus.1.aligned.dcd", "metadata": null, "mimetype": "application/octet-stream", "size": 64671540 }, "clus.1.dcd": { "checksum": "md5:25cf348f861b6f6cfd74023788843c02", "ext": "dcd", "id": "7a275f50-ba4a-4efc-bf65-51fdf0db2cf1", "key": "clus.1.dcd", "metadata": null, "mimetype": "application/octet-stream", "size": 64671540 }, "clus.1.pdb.gz": { "checksum": "md5:4c1d2289b3b2b337d55757729b95be7b", "ext": "gz", "id": "b855325d-52d2-4e0b-979c-060ddabac95f", "key": "clus.1.pdb.gz", "metadata": null, "mimetype": "application/gzip", "size": 96245209 }, "clus.2.aligned.dcd": { "checksum": "md5:55346bd30c89a660c7fcea2fd317f000", "ext": "dcd", "id": "9365541e-7474-49a6-9c95-912d1749d90e", "key": "clus.2.aligned.dcd", "metadata": null, "mimetype": "application/octet-stream", "size": 51973764 }, "clus.2.dcd": { "checksum": "md5:c0d70979b848c26c87c3d90a48d5f60a", "ext": "dcd", "id": "6e17aba1-4636-406b-8ac1-972d2765065a", "key": "clus.2.dcd", "metadata": null, "mimetype": "application/octet-stream", "size": 51973764 }, "clus.2.pdb.gz": { "checksum": "md5:cc45bbace4a16ae8b2ed7e7a8397c7a6", "ext": "gz", "id": "807ec568-fc9b-40cb-9949-0294aae6c428", "key": "clus.2.pdb.gz", "metadata": null, "mimetype": "application/gzip", "size": 77367899 }, "nup84-v1.0.3.zip": { "checksum": "md5:2535170260c118eb21909ac9ae455584", "ext": "zip", "id": "9ed037d6-1c28-49a4-915d-aa1864b1fd50", "key": "nup84-v1.0.3.zip", "metadata": null, "mimetype": "application/zip", "size": 14111333 } }, "order": [], "total_bytes": 509902722 }, "id": "1218053", "is_draft": false, "is_published": true, "links": { "access": "https://zenodo.org/api/records/1218053/access", "access_links": "https://zenodo.org/api/records/1218053/access/links", "access_request": "https://zenodo.org/api/records/1218053/access/request", "access_users": "https://zenodo.org/api/records/1218053/access/users", "archive": "https://zenodo.org/api/records/1218053/files-archive", "archive_media": "https://zenodo.org/api/records/1218053/media-files-archive", "communities": "https://zenodo.org/api/records/1218053/communities", "communities-suggestions": "https://zenodo.org/api/records/1218053/communities-suggestions", "doi": "https://doi.org/10.5281/zenodo.1218053", "draft": "https://zenodo.org/api/records/1218053/draft", "files": "https://zenodo.org/api/records/1218053/files", "latest": "https://zenodo.org/api/records/1218053/versions/latest", "latest_html": "https://zenodo.org/records/1218053/latest", "media_files": "https://zenodo.org/api/records/1218053/media-files", "parent": "https://zenodo.org/api/records/596089", "parent_doi": "https://zenodo.org/doi/10.5281/zenodo.596089", "parent_html": "https://zenodo.org/records/596089", "requests": "https://zenodo.org/api/records/1218053/requests", "reserve_doi": "https://zenodo.org/api/records/1218053/draft/pids/doi", "self": "https://zenodo.org/api/records/1218053", "self_doi": "https://zenodo.org/doi/10.5281/zenodo.1218053", "self_html": "https://zenodo.org/records/1218053", "self_iiif_manifest": "https://zenodo.org/api/iiif/record:1218053/manifest", "self_iiif_sequence": "https://zenodo.org/api/iiif/record:1218053/sequence/default", "versions": "https://zenodo.org/api/records/1218053/versions" }, "media_files": { "count": 0, "enabled": false, "entries": {}, "order": [], "total_bytes": 0 }, "metadata": { "contributors": [ { "affiliations": [ { "name": "University of California, San Francisco, United States." } ], "person_or_org": { "family_name": "Webb", "given_name": "Benjamin", "name": "Webb, Benjamin", "type": "personal" }, "role": { "id": "datamanager", "title": { "de": "DatenmanagerIn", "en": "Data manager" } } } ], "creators": [ { "affiliations": [ { "name": "Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065" } ], "person_or_org": { "family_name": "Shi", "given_name": "Yi", "name": "Shi, Yi", "type": "personal" } }, { "affiliations": [ { "name": "Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065" } ], "person_or_org": { "family_name": "Fernandez-Martinez", "given_name": "Javier", "name": "Fernandez-Martinez, Javier", "type": "personal" } }, { "affiliations": [ { "name": "Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158" } ], "person_or_org": { "family_name": "Tjioe", "given_name": "Elina", "name": "Tjioe, Elina", "type": "personal" } }, { "affiliations": [ { "name": "Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158" } ], "person_or_org": { "family_name": "Pellarin", "given_name": "Riccardo", "name": "Pellarin, Riccardo", "type": "personal" } }, { "affiliations": [ { "name": "Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158" } ], "person_or_org": { "family_name": "Kim", "given_name": "Seung Joong", "name": "Kim, Seung Joong", "type": "personal" } }, { "affiliations": [ { "name": "Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065" } ], "person_or_org": { "family_name": "Williams", "given_name": "Rosemary", "name": "Williams, Rosemary", "type": "personal" } }, { "affiliations": [ { "name": "Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158" } ], "person_or_org": { "family_name": "Schneidman-Duhovny", "given_name": "Dina", "name": "Schneidman-Duhovny, Dina", "type": "personal" } }, { "affiliations": [ { "name": "Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065" } ], "person_or_org": { "family_name": "Rout", "given_name": "Michael", "name": "Rout, Michael", "type": "personal" } }, { "affiliations": [ { "name": "Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158" } ], "person_or_org": { "family_name": "Sali", "given_name": "Andrej", "name": "Sali, Andrej", "type": "personal" } }, { "affiliations": [ { "name": "Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065" } ], "person_or_org": { "family_name": "Chait", "given_name": "Brian", "name": "Chait, Brian", "type": "personal" } } ], "description": "
These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the Nup84 complex using 286 DSS/EDC chemical cross-links and an electron microscopy (EM) 2D class average.
\n\nFirst, MODELLER is used to generate initial structures for the individual components in the Nup84 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class average for the entire Nup84 complex.
\n\nFor more information about how to reproduce this modeling, see the Sali lab website or the README file.
", "publication_date": "2014-08-26", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "https://github.com/integrativemodeling/nup84/tree/v1.0", "relation_type": { "id": "issupplementto", "title": { "de": "Erg\u00e4nzt", "en": "Is supplement to" } }, "scheme": "url" }, { "identifier": "10.1074/mcp.M114.041673", "relation_type": { "id": "issupplementto", "title": { "de": "Erg\u00e4nzt", "en": "Is supplement to" } }, "scheme": "doi" }, { "identifier": "10.5281/zenodo.580803", "relation_type": { "id": "isnewversionof", "title": { "de": "Ist eine neue Version von", "en": "Is new version of" } }, "scheme": "doi" }, { "identifier": "https://salilab.org/nup84", "relation_type": { "id": "issupplementto", "title": { "de": "Erg\u00e4nzt", "en": "Is supplement to" } }, "scheme": "url" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "" }, "id": "lgpl-2.1-only", "props": { "scheme": "spdx", "url": "https://www.gnu.org/licenses/old-licenses/lgpl-2.1-standalone.html" }, "title": { "en": "GNU Lesser General Public License v2.1 only" } } ], "subjects": [ { "subject": "Integrative Modeling Platform (IMP)" }, { "subject": "Chemical crosslinks" }, { "subject": "Electron microscopy class average" }, { "subject": "MODELLER" }, { "subject": "PMI" } ], "title": "Modeling of the Nup84 subcomplex of the Nuclear Pore Complex" }, "parent": { "access": { "owned_by": { "user": 20506 } }, "communities": { "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2016-02-19T01:07:35+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "0b38b9de-2850-4276-9828-7532c6348702", "links": {}, "metadata": { "curation_policy": "Any study using the IMP software can be deposited here.", "description": "Integrative modeling of proteins and their assemblies using disparate sources of experimental, theoretical, and statistical information, using the Integrative Modeling Platform (IMP) software.", "page": "", "title": "Integrative Modeling" }, "revision_id": 0, "slug": "integrativemodeling", "updated": "2016-08-25T07:52:53+00:00" }, { "access": { "member_policy": "open", "members_visibility": "public", "record_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2016-02-22T23:35:09+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "caabf620-b648-4d99-9d5c-b61cd80fa9f2", "links": {}, "metadata": { "curation_policy": "Any current or past member of the Sali lab can upload here.", "description": "Andrej Sali's research lab at the University of California San Francisco (UCSF)", "page": "", "title": "Sali Lab at UCSF" }, "revision_id": 0, "slug": "salilab", "updated": "2016-08-25T07:52:54+00:00" } ], "ids": [ "0b38b9de-2850-4276-9828-7532c6348702", "caabf620-b648-4d99-9d5c-b61cd80fa9f2" ] }, "id": "596089", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.596089", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.1218053", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:1218053", "provider": "oai" } }, "revision_id": 5, "stats": { "all_versions": { "data_volume": 34254384184.0, "downloads": 544, "unique_downloads": 305, "unique_views": 1480, "views": 1593 }, "this_version": { "data_volume": 9957955983.0, "downloads": 208, "unique_downloads": 128, "unique_views": 325, "views": 352 } }, "status": "published", "updated": "2020-01-24T19:26:08.803065+00:00", "versions": { "index": 5, "is_latest": true } }