{ "schema_version": "2.0", "record_type": "dataset", "tier": "practical", "slug": "bindingdb", "name": "BindingDB", "summary": { "en": "License: permissive, share-alike (CC-BY-3.0); Mdexa hosting: link-only. all parts permissive; conditions are the union of the parts Risk flag(s): derived.", "zh": "许可证声明：宽松，须相同方式共享（CC-BY-3.0）；本站处理：只链接原出处。各部分均宽松，条件取各部分的并集。来源风险标记：derived。" }, "systems": [ "modern-medicine" ], "domains": [ "pharmacy-drugs" ], "content_types": [ "database" ], "content_description": { "en": "Public web-accessible database of measured protein-ligand binding affinities between candidate drug-target proteins and small drug-like molecules, used in drug discovery and medicinal chemistry.", "zh": "公开的网络访问数据库，收录候选药物靶点蛋白与小分子类药物配体之间测定的结合亲和力数据，用于药物发现与药物化学。" }, "languages": [ "en" ], "modalities": [ "tabular" ], "size": { "raw": "3.2M data for 1.4M Compounds and 11.5K Targets", "measures": [] }, "publisher": "University of California San Diego (BindingDB)", "year": { "value": null, "raw": null }, "license": { "legacy_status": "pending", "spdx": "CC-BY-3.0", "commercial_use": "yes", "derivatives": "yes", "redistribution": "yes", "rationale": { "en": "all parts permissive; conditions are the union of the parts", "zh": "各部分均宽松，条件取各部分的并集" }, "evidence": [ { "location": "terms-page", "location_detail": { "en": "Statement found in snapshot s02 (page)", "zh": "在快照 s02（page）中找到的声明" }, "excerpt": "Data imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License .", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "verified_on": "2026-11-12", "snapshot_id": "s02", "observed": "page", "captured_by": "pipeline" }, { "location": "terms-page", "location_detail": { "en": "Statement found in snapshot s02 (page)", "zh": "在快照 s02（page）中找到的声明" }, "excerpt": "All data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License .", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "verified_on": "2026-11-12", "snapshot_id": "s02", "observed": "page", "captured_by": "pipeline" }, { "location": "dataset-page", "location_detail": { "en": "Part \"data imported from ChEMBL\" found in snapshot s02 (page)", "zh": "在快照 s02（page）中找到：Part \"data imported from ChEMBL\"" }, "excerpt": "Data imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "verified_on": "2026-11-12", "snapshot_id": "s02", "observed": "page", "captured_by": "pipeline" }, { "location": "dataset-page", "location_detail": { "en": "Part \"data curated by BindingDB staff\" found in snapshot s02 (page)", "zh": "在快照 s02（page）中找到：Part \"data curated by BindingDB staff\"" }, "excerpt": "All data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "verified_on": "2026-11-12", "snapshot_id": "s02", "observed": "page", "captured_by": "pipeline" } ], "license_conditions": [ "attribution", "share-alike" ], "license_parts": [ { "name": { "en": "Data imported from ChEMBL", "zh": "Data imported from ChEMBL" }, "spdx": "CC-BY-SA-3.0", "status": "permissive", "separable": true, "license_conditions": [ "attribution", "share-alike" ], "evidence": { "excerpt": "Data imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License .", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02" } }, { "name": { "en": "data curated by BindingDB staff", "zh": "data curated by BindingDB staff" }, "spdx": "CC-BY-3.0", "status": "permissive", "separable": true, "license_conditions": [ "attribution" ], "evidence": { "excerpt": "All data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License .", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02" } } ], "notes": { "en": "risk flag(s) derived: never eligible or hosted", "zh": "risk flag(s) derived: never eligible or hosted" } }, "license_status": "permissive", "hosting": "link-only", "hosting_reason": { "en": "License permissive, share-alike: all parts permissive; conditions are the union of the parts. Risk flag(s): derived. Link only.", "zh": "许可证宽松，须相同方式共享：各部分均宽松，条件取各部分的并集。来源风险标记：derived。只链接原出处。" }, "signoff": null, "risk_flags": [ "derived" ], "provenance": { "source_description": null, "upstream": [ { "slug": null, "name": "ChEMBL", "relation": "derived-from" }, { "slug": null, "name": "PubChem confirmatory BioAssays", "relation": "derived-from" } ] }, "known_issues": [], "preflight": { "status": "not-run" }, "access": { "mdexa_download": null, "external_urls": [ "https://www.bindingdb.org/", "https://www.bindingdb.org/rwd/bind/info.jsp" ], "notes": null }, "citation": { "text": null, "references": [] }, "verification_level": "verified", "last_verified": "2026-11-14", "tags": [ { "facet": "intended_use", "value": "evaluation", "basis": "author-stated", "excerpt": "To help with training and testing AI and other models, BindingDB downloads and search results now provide the publication date and BindingDB curation date of each measurement.", "snapshot_id": "s02" }, { "facet": "specialty", "value": "pharmacy", "basis": "inferred", "inferred_from": "card-content-description", "excerpt": "BindingDB supports research, education and practice in drug discovery, pharmacology and related fields.", "snapshot_id": "s02" }, { "facet": "source_type", "value": "literature", "basis": "author-stated", "excerpt": "BindingDB includes data extracted from the literature and patents by the BindingDB project", "snapshot_id": "s02" }, { "facet": "source_type", "value": "knowledge-base", "basis": "author-stated", "excerpt": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data", "snapshot_id": "s02" }, { "facet": "data_format", "value": "tsv", "basis": "inferred", "inferred_from": "card-content-description", "excerpt": "Documentation of BindingDB's SDfile and TSV formats", "snapshot_id": "s02" }, { "facet": "expert_involvement", "value": "per-item-review", "basis": "inferred", "inferred_from": "card-content-description", "excerpt": "1.6M data for 772K Compounds and 4.8K Targets were curated by BindingDB curators", "snapshot_id": "s02" } ], "changelog": [ { "date": "2026-11-13", "change": { "en": "Added via the automated pipeline and passed all checks (gates, verbatim quotes, rule engine, two independent extractions).", "zh": "经自动流水线收录并通过全部校验（门禁、逐字引用、判定引擎、两轮独立抽取）。" } }, { "date": "2026-11-13", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-13", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-13", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-13", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-13", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-13", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-13", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-13", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-13", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-14", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-14", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-14", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-14", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-14", "change": { "en": "Re-adjudicated under the current rules; all machine checks still pass.", "zh": "按当前规则重新判定；机器检查仍全部通过。" } }, { "date": "2026-11-14", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-14", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } }, { "date": "2026-11-14", "change": { "en": "Practical fields (scope, identifiers, access methods, versions, known defects) were added by the automated pipeline from stored page snapshots; every statement carries a verbatim quote.", "zh": "实用卡字段（内容范围、标识符、取用方式、版本、已知缺陷）由自动流水线根据已存快照添加，每条陈述带逐字引文。" } }, { "date": "2026-11-14", "change": { "en": "Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is.", "zh": "补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。" } } ], "practical": { "content_scope": { "entities": [ { "kind": "binding measurement (protein-ligand affinity data)", "count": 3241782, "count_as_of": null, "statement": { "text": { "en": "BindingDB holds about 3,241,782 binding data records covering 11,509 proteins and over 1,440,011 drug-like molecules.", "zh": "BindingDB 包含约 3,241,782 条结合数据，涵盖 11,509 个蛋白质和超过 1,440,011 个类药分子。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB currently contains about 3,241,782 binding data for 11,509 proteins and over 1,440,011 drug-like molecules.", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02", "char_start": 2128, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] } } ], "coverage": [ { "text": { "en": "Of that total, 1.6 million data records for 772 thousand compounds and 4.8 thousand targets were curated by BindingDB curators.", "zh": "其中 160 万条数据、77.2 万个化合物和 4.8 千个靶标是由 BindingDB 策展人员整理的。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Of those, 1.6M data for 772K Compounds and 4.8K Targets were curated by BindingDB curators.", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02", "char_start": 342, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] }, { "text": { "en": "The data collection comes from measurement techniques including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays.", "zh": "数据采集来自多种测量技术，包括酶抑制与动力学、等温滴定量热法、核磁共振以及放射配体和竞争分析。" }, "evidence": [ { "location": "dataset-page", "excerpt": "The data collection derives from a variety of measurement techniques, including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays.", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02", "char_start": 1606, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] }, { "text": { "en": "BindingDB includes data extracted from literature and patents by the project, selected PubChem confirmatory BioAssays, and ChEMBL entries with a well defined protein target.", "zh": "BindingDB 包含该项目从文献和专利中提取的数据、选定的 PubChem 确证性生物测定，以及具有明确定义蛋白质靶标的 ChEMBL 条目。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB includes data extracted from the literature and patents by the BindingDB project, selected PubChem confirmatory BioAssays, and ChEMBL entries for which a well defined protein target (\"TARGET_TYPE='PROTEIN'\") is provided.", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02", "char_start": 1797, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] }, { "text": { "en": "BindingDB also includes a small collection of host-guest binding data.", "zh": "BindingDB 还包含一小部分主客体结合数据。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB also includes a small collection of host-guest binding data of interest to chemists studying supramolecular systems.", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02", "char_start": 1478, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] } ] }, "identifiers": { "schemes": [ { "name": "BindingDB monomer (compound) ID", "bioregistry_prefix": null, "applies_to": "compounds", "statement": { "text": { "en": "BindingDB uses monomer (compound) IDs, which a download file maps to PubChem CIDs.", "zh": "BindingDB 使用单体（化合物）ID，并有一个下载文件将其映射到 PubChem CID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_CID.txt ( Mapping of BindingDB monomer (compound) IDs to PubChem CIDs. 23.67 MB, updated 2026-10-01)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 5966, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, { "name": "BindingDB polymer (single protein) ID", "bioregistry_prefix": null, "applies_to": "proteins", "statement": { "text": { "en": "BindingDB uses polymer (single protein) IDs, mapped to UniProt IDs in a download file.", "zh": "BindingDB 使用聚合物（单一蛋白质）ID，并在一个下载文件中映射到 UniProt ID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_UniProt.txt ( Mapping of BindingDB polymer (single protein) IDs to UniProt IDs. 572.93 KB, updated 2026-10-01)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 6513, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } } ], "crosswalks": [ { "to": "PubChem CIDs", "to_slug": null, "statement": { "text": { "en": "A download file maps BindingDB monomer (compound) IDs to PubChem CIDs.", "zh": "一个下载文件将 BindingDB 单体（化合物）ID 映射到 PubChem CID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_CID.txt ( Mapping of BindingDB monomer (compound) IDs to PubChem CIDs. 23.67 MB, updated 2026-10-01)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 5966, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, { "to": "PubChem SIDs", "to_slug": null, "statement": { "text": { "en": "A download file maps BindingDB monomer (compound) IDs to PubChem SIDs.", "zh": "一个下载文件将 BindingDB 单体（化合物）ID 映射到 PubChem SID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_SID.txt ( Mapping of BindingDB monomer (compound) IDs to PubChem SIDs. 24.44 MB, updated 2026-10-01)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 6077, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, { "to": "ChEBI", "to_slug": null, "statement": { "text": { "en": "A download file maps BindingDB monomer (compound) IDs to CHEBI IDs.", "zh": "一个下载文件将 BindingDB 单体（化合物）ID 映射到 CHEBI ID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_CHEBI_ID.txt ( Mapping of BindingDB monomer (compound) IDs to CHEBI IDs. 191.64 KB, updated 2026-10-01)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 6188, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, { "to": "DrugBank", "to_slug": null, "statement": { "text": { "en": "A download file maps BindingDB monomer (compound) IDs to DrugBank IDs.", "zh": "一个下载文件将 BindingDB 单体（化合物）ID 映射到 DrugBank ID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_DrugBankID.txt ( Mapping of BindingDB monomer (compound) IDs to DrugBank IDs. 41.02 KB, updated 2026-10-01)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 6302, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, { "to": "UniProt", "to_slug": null, "statement": { "text": { "en": "A download file maps BindingDB polymer (single protein) IDs to UniProt IDs.", "zh": "一个下载文件将 BindingDB 聚合物（单一蛋白质）ID 映射到 UniProt ID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_UniProt.txt ( Mapping of BindingDB polymer (single protein) IDs to UniProt IDs. 572.93 KB, updated 2026-10-01)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 6513, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, { "to": "PubMed", "to_slug": null, "statement": { "text": { "en": "A download file collects the PubMed IDs present in BindingDB.", "zh": "一个下载文件收集了 BindingDB 中的 PubMed ID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_PubMed.txt ( Collection of PubMed IDs in BindingDB. 396.56 KB, updated 2026-11-13)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 6420, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } } ], "mismatch_cases": [], "notes": [ { "text": { "en": "Downloads now include each measurement's publication date and BindingDB curation date, intended to support training and testing of AI models.", "zh": "下载文件现在附带每条测量的发表日期与 BindingDB 收录日期，官方称用于支持 AI 模型的训练与测试。" }, "evidence": [ { "location": "dataset-page", "excerpt": "To help with training and testing AI and other models, BindingDB downloads and search results now provide the publication date and BindingDB curation date of each measurement.", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes", "snapshot_id": "s08", "char_start": 904, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "BindingDB Downloads", "authors_or_org": "BindingDB", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes" } } ] } ] }, "access_methods": [ { "method": "web-api", "url": "https://www.bindingdb.org/rwd/bind/BindingDBRESTfulAPI.jsp", "formats": [ "JSON", "XML" ], "limits": [], "terms": { "same_as_card_license": true, "own_terms": null }, "reachable": { "status": 200, "checked_on": "2026-11-14" } }, { "method": "bulk-download", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "formats": [ "TSV" ], "limits": [], "terms": { "same_as_card_license": true, "own_terms": null }, "reachable": { "status": 200, "checked_on": "2026-11-14" } }, { "method": "database-dump", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "formats": [ "MySQL dump" ], "limits": [], "terms": { "same_as_card_license": true, "own_terms": null }, "reachable": { "status": 200, "checked_on": "2026-11-14" } }, { "method": "database-dump", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes", "formats": [], "limits": [], "terms": { "same_as_card_license": true, "own_terms": null }, "statement": { "text": { "en": "Bulk downloads are TSV (one row per measurement) and SDF, split by source (BindingDB-curated, ChEMBL, US patents, PubChem, PDSP Ki, CSAR); a MySQL dump is listed as beta, dated 2022-09-17.", "zh": "批量下载为 TSV（每行一条测量）与 SDF，按来源分包（BindingDB 自整理、ChEMBL、美国专利、PubChem、PDSP Ki、CSAR）；MySQL 转储标为测试版，日期 2022-09-17。" }, "evidence": [ { "location": "dataset-page", "excerpt": "MySQL DB: BDB_my.tar (1.9 GB, updated 2022-09-17; in beta-test)", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes", "snapshot_id": "s08", "char_start": 1731, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "BindingDB Downloads", "authors_or_org": "BindingDB", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes" } } ] }, "reachable": { "status": 200, "checked_on": "2026-11-14" } }, { "method": "web-ui-only", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/", "formats": [], "limits": [], "terms": { "same_as_card_license": true, "own_terms": null }, "statement": { "text": { "en": "Licensing is mixed: BindingDB-curated data are CC BY 4.0, while data imported from ChEMBL remain under ChEMBL's CC BY-SA 3.0 and are marked as ChEMBL-curated.", "zh": "许可是混合的：BindingDB 自行整理的数据为 CC BY 4.0，从 ChEMBL 导入的数据仍受 ChEMBL 的 CC BY-SA 3.0 约束，并标注为 ChEMBL 整理。" }, "evidence": [ { "location": "peer-reviewed-paper", "excerpt": "Thus, ChEMBL data in BindingDB are subject to the ChEMBL license, and they are marked as curated by ChEMBL to enable compliance.", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/", "snapshot_id": "s07", "char_start": 43301, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data", "authors_or_org": "Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK (Nucleic Acids Research)", "date": "2025-01-01", "date_as_written": "2025-01-01", "source_type": "peer-reviewed-paper", "open_access": true, "doi_or_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/" } } ] }, "reachable": { "status": 200, "checked_on": "2026-11-14" } } ], "versioning": { "latest": { "label": "202611 release (BindingDB_All_202611_tsv.zip)", "released_on": "2026-10-31", "statement": { "text": { "en": "The 202611 release file BindingDB_All_202611_tsv.zip is marked as updated 2026-10-31.", "zh": "202611 发布版文件 BindingDB_All_202611_tsv.zip 标注更新于 2026-10-31。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB_All_202611_tsv.zip ( 566.75 MB, updated 2026-10-31 ) md5", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 2701, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, "update_cycle": { "cycle": "monthly", "statement": { "text": { "en": "The download files are updated when new data are added, usually monthly.", "zh": "这些下载文件在有新数据加入时更新，通常每月一次。" }, "evidence": [ { "location": "dataset-page", "excerpt": "These files updated when new data are added, usually monthly", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 904, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, "breaking_changes": [ { "version": "BDB-Oracle_All_202502_dmp.zip", "date": null, "kind": "access", "statement": { "text": { "en": "The Oracle database dump BDB-Oracle_All_202502_dmp.zip is listed as Discontinued.", "zh": "Oracle 数据库转储 BDB-Oracle_All_202502_dmp.zip 被列为已停止提供。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Full BindingDB Database Dump Oracle DB: BDB-Oracle_All_202502_dmp.zip (Discontinued) ( 837.50 MB, updated 2025-03-26) md5", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp", "snapshot_id": "s05", "char_start": 2248, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } } ], "history_url": null, "notes": [ { "text": { "en": "Files are updated when new data are added, usually monthly; the 2024 paper says new BindingDB-curated data are released around the start of each month and ChEMBL updates are imported typically within a month.", "zh": "文件随新数据更新，通常每月一次；2024 年论文称自行整理的数据约在每月初发布，ChEMBL 新版通常在一个月内导入。" }, "evidence": [ { "location": "peer-reviewed-paper", "excerpt": "Each new tranche of data curated by BindingDB is released monthly, with updated data files available for download around the start of each calendar month.", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/", "snapshot_id": "s07", "char_start": 14009, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data", "authors_or_org": "Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK (Nucleic Acids Research)", "date": "2025-01-01", "date_as_written": "2025-01-01", "source_type": "peer-reviewed-paper", "open_access": true, "doi_or_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/" } } ] } ] }, "known_defects": [ { "kind": "data-quality", "statement": { "text": { "en": "BindingDB authors: the most common curation error (by BindingDB or ChEMBL) is a factor-of-1000 unit error, e.g. an IC50 curated as nM instead of µM.", "zh": "BindingDB 作者：最常见的整理错误（BindingDB 或 ChEMBL 造成）是 1000 倍单位错误，如把 µM 的 IC50 记成 nM。" }, "evidence": [ { "location": "peer-reviewed-paper", "excerpt": "These appear most commonly as a factor of 1000 error resulting from miscuration of e.g. an IC50 value as nanomolar instead of micromolar or vice versa .", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/", "snapshot_id": "s07", "char_start": 28370, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data", "authors_or_org": "Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK (Nucleic Acids Research)", "date": "2025-01-01", "date_as_written": "2025-01-01", "source_type": "peer-reviewed-paper", "open_access": true, "doi_or_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/" } } ] }, "source_kind": "peer-reviewed-paper", "scope": null, "attribution": { "who": "Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK (Nucleic Acids Research)", "when": "2025-01-01", "source_type": "peer-reviewed-paper", "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data" }, "correction_entrance": "Report an error through the publisher or the authors: https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/" }, { "kind": "data-quality", "statement": { "text": { "en": "BindingDB authors: the next most common reported error is misidentification of the protein target, usually when a document covers multiple targets or subtypes.", "zh": "BindingDB 作者：其次常见的是靶蛋白识别错误，多发生在一篇专利或文章涉及多个靶点或亚型时。" }, "evidence": [ { "location": "peer-reviewed-paper", "excerpt": "Based on user feedback, the next most common error appears to be misidentification of a protein target.", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/", "snapshot_id": "s07", "char_start": 28523, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data", "authors_or_org": "Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK (Nucleic Acids Research)", "date": "2025-01-01", "date_as_written": "2025-01-01", "source_type": "peer-reviewed-paper", "open_access": true, "doi_or_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/" } } ] }, "source_kind": "peer-reviewed-paper", "scope": null, "attribution": { "who": "Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK (Nucleic Acids Research)", "when": "2025-01-01", "source_type": "peer-reviewed-paper", "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data" }, "correction_entrance": "Report an error through the publisher or the authors: https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/" }, { "kind": "data-quality", "statement": { "text": { "en": "Errors in source patents or articles are hard for BindingDB to detect; they may show up only as outliers when the same affinity was measured more than once.", "zh": "来源专利或文章本身的错误 BindingDB 难以发现，只有同一亲和力被多次测量时才可能作为离群值显现。" }, "evidence": [ { "location": "peer-reviewed-paper", "excerpt": "Such errors are difficult for us to discover and hence correct, though they might be flagged as outliers in cases where the same protein-ligand affinity has been measured more than once.", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/", "snapshot_id": "s07", "char_start": 27783, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data", "authors_or_org": "Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK (Nucleic Acids Research)", "date": "2025-01-01", "date_as_written": "2025-01-01", "source_type": "peer-reviewed-paper", "open_access": true, "doi_or_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/" } } ] }, "source_kind": "peer-reviewed-paper", "scope": null, "attribution": { "who": "Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK (Nucleic Acids Research)", "when": "2025-01-01", "source_type": "peer-reviewed-paper", "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data" }, "correction_entrance": "Report an error through the publisher or the authors: https://pmc.ncbi.nlm.nih.gov/articles/PMC11701568/" } ], "fit": { "suited_for": [ { "text": { "en": "BindingDB states it supports medicinal chemistry and drug discovery through literature awareness and SAR/QSAR development, and validation of computational approaches such as docking, scoring and free energy methods.", "zh": "BindingDB 声明其通过文献追踪和 SAR/QSAR 开发，以及对接、打分和自由能方法等计算方法的验证，支持药物化学和药物发现。" }, "evidence": [ { "location": "dataset-page", "excerpt": "BindingDB supports medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of computational chemistry and molecular modeling approaches such as docking, scoring and free energy methods", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02", "char_start": 1099, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] }, { "text": { "en": "BindingDB downloads and search results provide the publication date and BindingDB curation date of each measurement to help with training and testing AI and other models.", "zh": "为帮助训练和测试 AI 及其他模型，BindingDB 下载数据和搜索结果提供每条测定的出版日期与 BindingDB 策展日期。" }, "evidence": [ { "location": "dataset-page", "excerpt": "To help with training and testing AI and other models, BindingDB downloads and search results now provide the publication date and BindingDB curation date of each measurement.", "url": "https://www.bindingdb.org/rwd/bind/info.jsp", "snapshot_id": "s02", "char_start": 681, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] } ], "not_suited_for": [] }, "commercial_access": { "route": "unknown", "url": null, "statement": null }, "completeness": { "core_complete": true, "literature_defects": 3, "reachable_access": 5, "meets_practical_bar": true, "gaps": [ { "field": "fit.not_suited_for", "note": "未找到有出处的说明 / no sourced statement found" }, { "field": "commercial_access", "note": "未找到有出处的说明 / no sourced statement found" } ] } }, "access_recipe": { "verified_on": "2026-11-14", "latest_release": null, "files": [], "api": [ { "name": "getLigandsByUniprot", "url_template": "https://bindingdb.org/rest/getLigandsByUniprot?uniprot={UNIPROT};{IC50cutoff}", "required_params": [ "UNIPROT" ], "example_request": "https://bindingdb.org/rest/getLigandsByUniprot?uniprot=P35355;100&response=application/json", "key_response_fields": [ "monomerIDs", "SMILES strings", "affinity types", "affinity values" ], "evidence": { "excerpt": "https://bindingdb.org/rest/getLigandsByUniprot?uniprot={UNIPROT};{IC50cutoff}", "snapshot_id": "s03", "url": "https://www.bindingdb.org/rwd/bind/BindingDBRESTfulAPI.jsp" } } ], "registration": null, "bulk_download": [], "gaps": [ "no direct file address was found on the official pages we hold", "no latest release/version stated on the pages we hold", "the official pages we hold publish no checksum for the files; none was computed (we do not download data files)" ], "license_note": { "license_status": "permissive", "text": "Use according to the terms of the official source; this recipe does not say the data can be used freely." } }, "_links": { "text": "Continue in this database. This record is one of 109 processed and verified records (datasets, data resources and open models). To find others, call `https://mcp.mdexa.com/v1/datasets?q=` or connect the MCP server at `https://mcp.mdexa.com/mcp`; no key is needed for 20 calls per minute. Rows are under 1 KB; an empty result means \"not listed\". For a list of items, one batch check (free account) returns a report. Guide: /agents.md. Similar records: TopU-LBVS: Multi-Target Benchmark for Ligand-Based Virtual Screening (https://mdexa.com/datasets/topu-lbvs/); Therapeutics Data Commons (https://mdexa.com/datasets/tdc/); ChEMBL (https://mdexa.com/datasets/chembl/).", "records": 109, "search": { "template": "https://mcp.mdexa.com/v1/datasets?q={words}", "example": "https://mcp.mdexa.com/v1/datasets?q=binding%20affinity" }, "mcp": "https://mcp.mdexa.com/mcp", "anonymous_calls_per_minute": 20, "guide": "https://mdexa.com/agents.md", "faq": "https://mdexa.com/developers/faq/", "similar": [ { "name": "TopU-LBVS: Multi-Target Benchmark for Ligand-Based Virtual Screening", "url": "https://mdexa.com/datasets/topu-lbvs/", "json": "https://mdexa.com/datasets/topu-lbvs.json" }, { "name": "Therapeutics Data Commons", "url": "https://mdexa.com/datasets/tdc/", "json": "https://mdexa.com/datasets/tdc.json" }, { "name": "ChEMBL", "url": "https://mdexa.com/datasets/chembl/", "json": "https://mdexa.com/datasets/chembl.json" } ] } }