Changes

On December 2, 2024 at 11:32:57 PM UTC, admin:
Changed title to PDBBind (previously PDBbind)
Set author of PDBBind to Z Liu (previously Junde Li)
Updated description of PDBBind from
The dataset is used for compound-protein binding affinity prediction, and it contains 12,699 compound-protein pairs.
to
A dataset of 3D structures of about 10k complexes, i.e., structures of ligands docked in binding pockets of proteins.
Removed the following tags from PDBBind
Added the following tags to PDBBind
Changed value of field defined_in to in PDBBind
Changed value of field extra_authors to [{'extra_author': 'Y Li', 'orcid': ''}, {'extra_author': 'L Han', 'orcid': ''}, {'extra_author': 'J Li', 'orcid': ''}, {'extra_author': 'J Liu', 'orcid': ''}, {'extra_author': 'Z Zhao', 'orcid': ''}, {'extra_author': 'W Nie', 'orcid': ''}, {'extra_author': 'Y Liu', 'orcid': ''}, {'extra_author': 'R Wang', 'orcid': ''}] in PDBBind
Changed value of field citation to [] in PDBBind
Changed value of field landing_page to https://doi.org/10.1038/ncomms5094 in PDBBind
Deleted resource Original Metadata from PDBBind
              
    
          
          
        
        
            f 1 { f 1 {
            2   "access_rights": "", 2   "access_rights": "",
            n 3   "author": "Junde Li", n 3   "author": "Z Liu",
            4   "author_email": "", 4   "author_email": "",
            n 5   "citation": [ n 5   "citation": [],
            6     "https://doi.org/10.48550/arXiv.2112.12563", 
            7     "https://doi.org/10.48550/arXiv.2311.18574" 
            8   ], 
            9   "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700", 6   "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700",
            n 10   "defined_in": "https://doi.org/10.48550/arXiv.2204.12586", n 7   "defined_in": "",
            11   "doi": "10.57702/k1e8e089", 8   "doi": "10.57702/k1e8e089",
            12   "doi_date_published": "2024-12-02", 9   "doi_date_published": "2024-12-02",
            13   "doi_publisher": "TIB", 10   "doi_publisher": "TIB",
            14   "doi_status": true, 11   "doi_status": true,
            15   "domain": "https://service.tib.eu/ldmservice", 12   "domain": "https://service.tib.eu/ldmservice",
            16   "extra_authors": [ 13   "extra_authors": [
            17     { 14     {
            n n 15       "extra_author": "Y Li",
            16       "orcid": ""
            17     },
            18     {
            19       "extra_author": "L Han",
            20       "orcid": ""
            21     },
            22     {
            23       "extra_author": "J Li",
            24       "orcid": ""
            25     },
            26     {
            27       "extra_author": "J Liu",
            28       "orcid": ""
            29     },
            30     {
            18       "extra_author": "Swaroop Ghosh", 31       "extra_author": "Z Zhao",
            32       "orcid": ""
            33     },
            34     {
            35       "extra_author": "W Nie",
            36       "orcid": ""
            37     },
            38     {
            39       "extra_author": "Y Liu",
            40       "orcid": ""
            41     },
            42     {
            43       "extra_author": "R Wang",
            19       "orcid": "" 44       "orcid": ""
            20     } 45     }
            21   ], 46   ],
            22   "groups": [ 47   "groups": [
            23     { 48     {
            24       "description": "", 49       "description": "",
            n 25       "display_name": "Bioinformatics", n 50       "display_name": "Structure-based Virtual Screening",
            26       "id": "8873e69c-aaa7-49c3-9aa0-09c38b25a369", 51       "id": "f5bc295b-ead2-439a-880c-531c87a39744",
            27       "image_display_url": "", 52       "image_display_url": "",
            n 28       "name": "bioinformatics", n 53       "name": "structure-based-virtual-screening",
            29       "title": "Bioinformatics" 54       "title": "Structure-based Virtual Screening"
            30     }, 55     },
            31     { 56     {
            32       "description": "", 57       "description": "",
            n 33       "display_name": "Chemistry", n 58       "display_name": "Virtual Screening",
            34       "id": "c0f36b78-cd17-4792-8301-60807bc5a9ac", 59       "id": "85ce3c3f-4655-4292-ab9d-ef06335fc78b",
            35       "image_display_url": "", 60       "image_display_url": "",
            n 36       "name": "chemistry", n 61       "name": "virtual-screening",
            37       "title": "Chemistry" 62       "title": "Virtual Screening"
            38     }, 
            39     { 
            40       "description": "", 
            41       "display_name": "Drug Discovery", 
            42       "id": "36599ef1-90c1-4573-91d8-81b89c49184e", 
            43       "image_display_url": "", 
            44       "name": "drug-discovery", 
            45       "title": "Drug Discovery" 
            46     }, 
            47     { 
            48       "description": "", 
            49       "display_name": "Molecular Docking", 
            50       "id": "31599798-a839-4a9c-a250-d865b5822c2b", 
            51       "image_display_url": "", 
            52       "name": "molecular-docking", 
            53       "title": "Molecular Docking" 
            54     }, 
            55     { 
            56       "description": "", 
            57       "display_name": "Molecules", 
            58       "id": "37bea1cd-19ae-40e3-8053-be65bd82c3b1", 
            59       "image_display_url": "", 
            60       "name": "molecules", 
            61       "title": "Molecules" 
            62     }, 
            63     { 
            64       "description": "", 
            65       "display_name": "Protein-ligand complexes", 
            66       "id": "53b5a02b-5f1f-4fe3-a34a-7a9516f0ef1d", 
            67       "image_display_url": "", 
            68       "name": "protein-ligand-complexes", 
            69       "title": "Protein-ligand complexes" 
            70     } 63     }
            71   ], 64   ],
            72   "id": "16b45565-d138-44d4-9e02-a9e27c0739fa", 65   "id": "16b45565-d138-44d4-9e02-a9e27c0739fa",
            73   "isopen": false, 66   "isopen": false,
            n 74   "landing_page": "https://doi.org/10.1039/C9CC90091F", n 67   "landing_page": "https://doi.org/10.1038/ncomms5094",
            75   "license_title": null, 68   "license_title": null,
            76   "link_orkg": "", 69   "link_orkg": "",
            77   "metadata_created": "2024-12-02T17:56:25.746208", 70   "metadata_created": "2024-12-02T17:56:25.746208",
            n 78   "metadata_modified": "2024-12-02T17:56:26.102138", n 71   "metadata_modified": "2024-12-02T23:32:56.530903",
            79   "name": "pdbbind", 72   "name": "pdbbind",
            n 80   "notes": "The dataset is used for compound-protein binding affinity  n 73   "notes": "A dataset of 3D structures of about 10k complexes, i.e., 
            81 prediction, and it contains 12,699 compound-protein pairs.", 74 structures of ligands docked in binding pockets of proteins.",
            82   "num_resources": 1, 75   "num_resources": 0,
            83   "num_tags": 9, 76   "num_tags": 3,
            84   "organization": { 77   "organization": {
            85     "approval_status": "approved", 78     "approval_status": "approved",
            86     "created": "2024-11-25T12:11:38.292601", 79     "created": "2024-11-25T12:11:38.292601",
            87     "description": "", 80     "description": "",
            88     "id": "079d46db-32df-4b48-91f3-0a8bc8f69559", 81     "id": "079d46db-32df-4b48-91f3-0a8bc8f69559",
            89     "image_url": "", 82     "image_url": "",
            90     "is_organization": true, 83     "is_organization": true,
            91     "name": "no-organization", 84     "name": "no-organization",
            92     "state": "active", 85     "state": "active",
            93     "title": "No Organization", 86     "title": "No Organization",
            94     "type": "organization" 87     "type": "organization"
            95   }, 88   },
            96   "owner_org": "079d46db-32df-4b48-91f3-0a8bc8f69559", 89   "owner_org": "079d46db-32df-4b48-91f3-0a8bc8f69559",
            97   "private": false, 90   "private": false,
            98   "relationships_as_object": [], 91   "relationships_as_object": [],
            99   "relationships_as_subject": [], 92   "relationships_as_subject": [],
            n 100   "resources": [ n 93   "resources": [],
            101     { 
            102       "cache_last_updated": null, 
            103       "cache_url": null, 
            104       "created": "2024-12-02T18:38:42", 
            105       "data": [ 
            106         "dcterms:title", 
            107         "dcterms:accessRights", 
            108         "dcterms:creator", 
            109         "dcterms:description", 
            110         "dcterms:issued", 
            111         "dcterms:language", 
            112         "dcterms:identifier", 
            113         "dcat:theme", 
            114         "dcterms:type", 
            115         "dcat:keyword", 
            116         "dcat:landingPage", 
            117         "dcterms:hasVersion", 
            118         "dcterms:format", 
            119         "mls:task", 
            120         "datacite:isDescribedBy" 
            121       ], 
            122       "description": "The json representation of the dataset with its  
            123 distributions based on DCAT.", 
            124       "format": "JSON", 
            125       "hash": "", 
            126       "id": "502214b0-0947-45a8-a3c9-e8d84d407892", 
            127       "last_modified": "2024-12-02T17:56:26.093917", 
            128       "metadata_modified": "2024-12-02T17:56:26.104815", 
            129       "mimetype": "application/json", 
            130       "mimetype_inner": null, 
            131       "name": "Original Metadata", 
            132       "package_id": "16b45565-d138-44d4-9e02-a9e27c0739fa", 
            133       "position": 0, 
            134       "resource_type": null, 
            135       "size": 1117, 
            136       "state": "active", 
            137       "url":  
            138 resource/502214b0-0947-45a8-a3c9-e8d84d407892/download/metadata.json", 
            139       "url_type": "upload" 
            140     } 
            141   ], 
            142   "services_used_list": "", 94   "services_used_list": "",
            143   "state": "active", 95   "state": "active",
            144   "tags": [ 96   "tags": [
            145     { 97     {
            n 146       "display_name": "Drug discovery", n 98       "display_name": "PDBBind",
            147       "id": "8dbbd679-b2f4-44bf-938a-a2571ea3c5db", 99       "id": "56bd7936-6330-46a3-b7a5-cf9f2a8b4795",
            148       "name": "Drug discovery", 100       "name": "PDBBind",
            149       "state": "active", 101       "state": "active",
            150       "vocabulary_id": null 102       "vocabulary_id": null
            151     }, 103     },
            152     { 104     {
            n 153       "display_name": "Molecules", n 105       "display_name": "Structure-based Virtual Screening",
            154       "id": "7526901e-8646-4910-89a7-69b416f1477b", 106       "id": "12f7daff-78c2-4f06-9bc3-1730434f7cd0",
            155       "name": "Molecules", 107       "name": "Structure-based Virtual Screening",
            156       "state": "active", 108       "state": "active",
            157       "vocabulary_id": null 109       "vocabulary_id": null
            158     }, 110     },
            159     { 111     {
            n 160       "display_name": "PDBbind", n 112       "display_name": "Virtual Screening",
            161       "id": "de23bfdd-2fab-4893-b578-0be7bd0c3fb8", 113       "id": "ae9d4cc8-7f62-4a36-bbfd-531840811e9a",
            162       "name": "PDBbind", 114       "name": "Virtual Screening",
            163       "state": "active", 
            164       "vocabulary_id": null 
            165     }, 
            166     { 
            167       "display_name": "Protein-ligand complexes", 
            168       "id": "bb45cce7-1753-43da-9f0e-27f31004b606", 
            169       "name": "Protein-ligand complexes", 
            170       "state": "active", 
            171       "vocabulary_id": null 
            172     }, 
            173     { 
            174       "display_name": "compound-protein binding affinity", 
            175       "id": "23da0098-4b85-4511-9eb1-b25cd387be01", 
            176       "name": "compound-protein binding affinity", 
            177       "state": "active", 
            178       "vocabulary_id": null 
            179     }, 
            180     { 
            181       "display_name": "drug discovery", 
            182       "id": "c0525e95-673f-4eae-bb86-c67d02d455d4", 
            183       "name": "drug discovery", 
            184       "state": "active", 
            185       "vocabulary_id": null 
            186     }, 
            187     { 
            188       "display_name": "molecular docking", 
            189       "id": "bdae7b57-6fd4-4c51-abfb-6d526948ca32", 
            190       "name": "molecular docking", 
            191       "state": "active", 
            192       "vocabulary_id": null 
            193     }, 
            194     { 
            195       "display_name": "protein-ligand complexes", 
            196       "id": "70ca5562-587f-4f27-93cc-0f389ba8973e", 
            197       "name": "protein-ligand complexes", 
            198       "state": "active", 
            199       "vocabulary_id": null 
            200     }, 
            201     { 
            202       "display_name": "protein-ligand interaction", 
            203       "id": "62873485-ff9a-4c12-8192-d7ec515db59d", 
            204       "name": "protein-ligand interaction", 
            205       "state": "active", 115       "state": "active",
            206       "vocabulary_id": null 116       "vocabulary_id": null
            207     } 117     }
            208   ], 118   ],
            t 209   "title": "PDBbind", t 119   "title": "PDBBind",
            210   "type": "dataset", 120   "type": "dataset",
            211   "version": "" 121   "version": ""
            212 } 122 }