{ "schema_version": "2.0", "record_type": "dataset", "tier": "verified", "slug": "rcsb-pdb", "name": "RCSB Protein Data Bank", "summary": { "en": "License: permissive (CC0-1.0); Mdexa hosting: link-only. all parts permissive; conditions are the union of the parts", "zh": "许可证声明：宽松（CC0-1.0）；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。" }, "systems": [ "modern-medicine" ], "domains": [ "genomics-omics" ], "content_types": [ "database" ], "content_description": { "en": "RCSB PDB enables scientific breakthroughs via tools for searching, visualization, and analysis of 3D structural data, and is a member of the Worldwide PDB partnership.", "zh": "RCSB PDB 通过检索、可视化与分析三维结构数据的工具推动科学发现，是世界蛋白质数据库合作组织的成员。" }, "languages": [ "en" ], "modalities": [ "text" ], "size": { "raw": null, "measures": [] }, "publisher": "RCSB PDB (wwPDB)", "year": { "value": 1971, "raw": "1971" }, "license": { "legacy_status": "pending", "spdx": "CC0-1.0", "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": "The wwPDB policy states that data files contained in the PDB archive are available under the CC0 1.0 Univer", "spdx": "CC0-1.0", "url": "https://www.rcsb.org/pages/policies", "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": "Data provided by RCSB PDB programmatic APIs are available under the same license unless they originate from an integrated external resource , in which case the licensing restrictions applied by the data provider must be followed.", "url": "https://www.rcsb.org/pages/policies", "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": "RCSB PDB software products are distributed under the terms of an open source license ( MIT or Apache 2.0 ).", "url": "https://www.rcsb.org/pages/policies", "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": "Molecule of the Month articles are copyrighted by RCSB PDB and the article authors. Text can be reprinted with permission, with attribution, and without the right to manipulate or change content.", "url": "https://www.rcsb.org/pages/policies", "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": "Molecule of the Month illustrations are available under a CC-BY-4.0 license .", "spdx": "CC-BY-4.0", "url": "https://www.rcsb.org/pages/policies", "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": "PDB-101 content is free for use under a CC-BY-4.0 license", "spdx": "CC-BY-4.0", "url": "https://www.rcsb.org/pages/policies", "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": "Global Health articles are copyrighted by RCSB PDB and the article authors.", "url": "https://www.rcsb.org/pages/policies", "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": "Other RCSB.org content ( e.g. , user guide documentation, statistics graphs, other screenshots) is available under a CC-BY-4.0 license .", "spdx": "CC-BY-4.0", "url": "https://www.rcsb.org/pages/policies", "verified_on": "2026-11-12", "snapshot_id": "s02", "observed": "page", "captured_by": "pipeline" }, { "location": "dataset-page", "location_detail": { "en": "Part \"integrated external resource\" found in snapshot s02 (page)", "zh": "在快照 s02（page）中找到：Part \"integrated external resource\"" }, "excerpt": "unless they originate from an integrated external resource , in which case the licensing restrictions applied by the data provider must be followed.", "url": "https://www.rcsb.org/pages/policies", "verified_on": "2026-11-12", "snapshot_id": "s02", "observed": "page", "captured_by": "pipeline" } ], "license_conditions": [ "attribution", "notice-required" ], "license_parts": [ { "name": { "en": "data files contained in the PDB archive", "zh": "data files contained in the PDB archive" }, "spdx": "CC0-1.0", "status": "permissive", "separable": true, "evidence": { "excerpt": "The wwPDB policy states that data files contained in the PDB archive are available under the CC0 1.0 Univer", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02" } }, { "name": { "en": "RCSB PDB programmatic APIs", "zh": "RCSB PDB programmatic APIs" }, "spdx": "CC0-1.0", "status": "permissive", "separable": true, "evidence": { "excerpt": "Data provided by RCSB PDB programmatic APIs are available under the same license unless they originate from an integrated external resource , in which case the licensing restrictions applied by the data provider must be followed.", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02" } }, { "name": { "en": "RCSB PDB software products", "zh": "RCSB PDB software products" }, "spdx": "Apache-2.0", "status": "permissive", "separable": true, "license_conditions": [ "notice-required" ], "evidence": { "excerpt": "RCSB PDB software products are distributed under the terms of an open source license ( MIT or Apache 2.0 ).", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02" } }, { "name": { "en": "Molecule of the Month illustrations", "zh": "Molecule of the Month illustrations" }, "spdx": "CC-BY-4.0", "status": "permissive", "separable": true, "license_conditions": [ "attribution" ], "evidence": { "excerpt": "Molecule of the Month illustrations are available under a CC-BY-4.0 license .", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02" } }, { "name": { "en": "PDB-101 content", "zh": "PDB-101 content" }, "spdx": "CC-BY-4.0", "status": "permissive", "separable": true, "license_conditions": [ "attribution" ], "evidence": { "excerpt": "PDB-101 content is free for use under a CC-BY-4.0 license", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02" } }, { "name": { "en": "Other RCSB.org content", "zh": "Other RCSB.org content" }, "spdx": "CC-BY-4.0", "status": "permissive", "separable": true, "license_conditions": [ "attribution" ], "evidence": { "excerpt": "Other RCSB.org content ( e.g. , user guide documentation, statistics graphs, other screenshots) is available under a CC-BY-4.0 license .", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02" } } ], "notes": { "en": "third-party copyright notice present: Molecule of the Month articles are copyrighted by RCSB PDB and the article authors. Text can be repr", "zh": "third-party copyright notice present: Molecule of the Month articles are copyrighted by RCSB PDB and the article authors. Text can be repr" } }, "license_status": "permissive", "hosting": "link-only", "hosting_reason": { "en": "License permissive: all parts permissive; conditions are the union of the parts. Link only.", "zh": "许可证宽松：各部分均宽松，条件取各部分的并集。只链接原出处。" }, "signoff": null, "risk_flags": [], "provenance": { "source_description": null, "upstream": [] }, "known_issues": [], "preflight": { "status": "not-run" }, "access": { "mdexa_download": null, "external_urls": [ "https://www.rcsb.org/", "https://www.rcsb.org/pages/policies" ], "notes": null }, "citation": { "text": null, "references": [ "10.1093/nar/28.1.235", "10.1093/nar/gkae1091", "10.1093/nar/gky949" ] }, "verification_level": "verified", "last_verified": "2026-11-14", "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": "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": "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": "macromolecular structure", "count": null, "count_as_of": null, "statement": { "text": { "en": "Since 1971 the PDB archive has been described as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.", "zh": "自1971年以来，PDB档案一直被称为蛋白质、核酸和复杂组装体三维结构信息的单一存储库。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.", "url": "https://www.wwpdb.org/", "snapshot_id": "s04", "char_start": 909, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } } ], "coverage": [ { "text": { "en": "Coordinate sets produced by X-ray crystallography, NMR, electron microscopy, neutron diffraction, powder diffraction, and fiber diffraction can be deposited to the PDB, provided the molecule studied meets the minimum size requirement.", "zh": "由X射线晶体学、核磁共振、电子显微镜、中子衍射、粉末衍射和纤维衍射产生的坐标集，只要所研究的分子满足最小尺寸要求，就可以存入PDB。" }, "evidence": [ { "location": "terms-page", "excerpt": "Currently, coordinate sets produced by X-ray crystallography, NMR, electron microscopy, neutron diffraction, powder diffraction, and fiber diffraction can be deposited to the PDB, provided the molecule studied meets the minimum size requirement.", "url": "https://www.wwpdb.org/documentation/policy", "snapshot_id": "s05", "char_start": 8776, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } ] }, "identifiers": { "schemes": [ { "name": "PDB ID", "bioregistry_prefix": null, "applies_to": "PDB entries", "statement": { "text": { "en": "PDB entries are assigned a PDB ID and are frequently described in a publication by the structure authors.", "zh": "PDB条目会被分配一个PDB ID，并且常由结构作者在出版物中描述。" }, "evidence": [ { "location": "terms-page", "excerpt": "PDB entries are assigned a PDB ID and are frequently described in a publication by the structure authors.", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02", "char_start": 2212, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] } }, { "name": "entry_id", "bioregistry_prefix": null, "applies_to": "core_entry objects for PDB entries and Computed Structure Models", "statement": { "text": { "en": "The core_entry object covers a PDB entry or Computed Structure Model and is identified by an entry_id, which can be an alphanumeric PDB-ID or a CSM-ID starting with AF_ or MA_.", "zh": "core_entry对象对应PDB条目或计算结构模型，由entry_id标识，该标识可以是字母数字PDB-ID，或以AF_或MA_开头的CSM-ID。" }, "evidence": [ { "location": "api-doc", "excerpt": "core_entry : data that relates to a PDB entry or Computed Structure Model (CSM). Identified by an entry_id, which can be an alphanumeric PDB-ID or a CSM-ID that starts with AF_ or MA_", "url": "https://www.rcsb.org/docs/programmatic-access/web-apis-overview", "snapshot_id": "s03", "char_start": 5775, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, { "name": "chem_comp_id", "bioregistry_prefix": null, "applies_to": "chemical components", "statement": { "text": { "en": "The core_chem_comp object is a chemical component identified by a unique alphanumeric code chem_comp_id.", "zh": "core_chem_comp对象是化学组分，由唯一的字母数字代码chem_comp_id标识。" }, "evidence": [ { "location": "api-doc", "excerpt": "core_chem_comp : a chemical component. Identified by a unique alphanumeric code chem_comp_id", "url": "https://www.rcsb.org/docs/programmatic-access/web-apis-overview", "snapshot_id": "s03", "char_start": 6782, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } } ], "crosswalks": [ { "to": "NCBI RefSeq and UniProt", "to_slug": null, "statement": { "text": { "en": "The Sequence Coordinates API provides alignments between structural and sequence databases, with alignment data available for NCBI RefSeq, UniProt and PDB sequences.", "zh": "Sequence Coordinates API提供结构数据库与序列数据库之间的比对，比对数据涵盖NCBI RefSeq、UniProt和PDB序列。" }, "evidence": [ { "location": "api-doc", "excerpt": "The Sequence Coordinates API provides alignments between structural and sequence databases and integrates protein positional features from multiple resources. Alignment data is available for NCBI RefSeq (including protein and genomic sequences), UniProt and PDB sequences.", "url": "https://www.rcsb.org/docs/programmatic-access/web-apis-overview", "snapshot_id": "s03", "char_start": 9651, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } } ], "mismatch_cases": [], "notes": [ { "text": { "en": "wwPDB extended the PDB ID format by prefixing 'pdb_' and zero-padding (1abc becomes pdb_00001abc).", "zh": "wwPDB 将 PDB ID 扩展为加“pdb_”前缀并补零的格式（1abc 变为 pdb_00001abc）。" }, "evidence": [ { "location": "official-change-notice", "excerpt": "wwPDB has revised the PDB accession code format by extending its length and prepending", "url": "https://www.wwpdb.org/news/news?year=2024", "snapshot_id": "s10", "char_start": 57472, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Resources for Supporting the Extended PDB ID Format (pdb_00001abc)", "authors_or_org": "wwPDB", "date": "2024-01-08", "date_as_written": "2024-01-08", "source_type": "official-change-notice", "open_access": true, "doi_or_url": "https://www.wwpdb.org/news/news?year=2024" } } ] }, { "text": { "en": "Entries with 12-character extended IDs will exist only in PDBx/mmCIF, not in the legacy PDB format; wwPDB gave 2028 as the expected exhaustion of 4-character IDs in a June 2024 notice (its January 2024 notice said 2029).", "zh": "12 位扩展 ID 的条目只提供 PDBx/mmCIF，不提供旧 PDB 格式；wwPDB 2024 年 6 月公告预计 4 位 ID 于 2028 年耗尽（同年 1 月公告写的是 2029 年）。" }, "evidence": [ { "location": "official-change-notice", "excerpt": "The wwPDB anticipates that all four-character PDB IDs will be exhausted by 2028, after which 12-character PDB IDs will be issued. Entries with extended PDB IDs will not be compatible with the legacy PDB file format and will only be available in PDBx/mmCIF format.", "url": "https://www.wwpdb.org/news/news?year=2024", "snapshot_id": "s10", "char_start": 21022, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Announcing the New PDBx/mmCIF User Guide", "authors_or_org": "wwPDB", "date": "2024-06-18", "date_as_written": "2024-06-18", "source_type": "official-change-notice", "open_access": true, "doi_or_url": "https://www.wwpdb.org/news/news?year=2024" } } ] }, { "text": { "en": "RCSB documentation now shows IDs in the pdb_00001abc form and says entries deposited before 21 July 2027 will also keep a 4-character ID.", "zh": "RCSB 文档已用 pdb_00001abc 形式展示 ID，并说明 2027-07-21 前收存的条目同时保留 4 位 ID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "PDB ID for the entry (pdb_00001abc) . Entries deposited before July 21, 2027 will additionally have a 4-character ID.", "url": "https://www.rcsb.org/docs/general-help/identifiers-in-pdb", "snapshot_id": "s11", "char_start": 5543, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Identifiers in PDB", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/docs/general-help/identifiers-in-pdb" } } ] }, { "text": { "en": "A chain can carry two different IDs, shown as 'X [auth Y]', because PDB uses two chain-labelling systems (author 'auth' and PDB-assigned 'label').", "zh": "同一条链可能有两个链 ID（显示为“X [auth Y]”），因为 PDB 并用作者编号（auth）与 PDB 指派编号（label）两套体系。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Sometimes in structures available from RCSB.org may have two different chain identifiers (IDs) listed for a biopolymer or ligand, in the form X [auth Y] . This is because the PDB uses two distinct systems for labeling chain IDs.", "url": "https://www.rcsb.org/docs/general-help/identifiers-in-pdb", "snapshot_id": "s11", "char_start": 16011, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Identifiers in PDB", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/docs/general-help/identifiers-in-pdb" } } ] }, { "text": { "en": "Large series of related structures (e.g. one protein with many inhibitors) also receive a Group ID in addition to their PDB IDs.", "zh": "成批提交的相关结构（如同一蛋白结合多个抑制剂）除 PDB ID 外还有一个 Group ID。" }, "evidence": [ { "location": "dataset-page", "excerpt": "In addition to PDB IDs these structures have an additional identifier, called the Group ID ( e.g., G_1002018 ).", "url": "https://www.rcsb.org/docs/general-help/identifiers-in-pdb", "snapshot_id": "s11", "char_start": 8017, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Identifiers in PDB", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/docs/general-help/identifiers-in-pdb" } } ] } ] }, "access_methods": [ { "method": "web-api", "url": "https://www.rcsb.org/docs/programmatic-access/web-apis-overview", "formats": [ "JSON" ], "limits": [ { "text": { "en": "All RCSB PDB APIs have rate limits in place; the page suggests starting with a handful of requests per second, and exceeding the limit returns a 429 HTTP error code indicating that the request rate must be reduced.", "zh": "所有RCSB PDB API都设有速率限制；页面建议从每秒少量请求开始，超出限制时服务会返回429 HTTP错误码，提示需要降低请求速率。" }, "evidence": [ { "location": "api-doc", "excerpt": "all RCSB PDB APIs have rate limits in place. We recommend starting with a handful of requests per second. If you exceed the limit, the service will respond with a 429 HTTP error code, indicating that you need to reduce your request rate as described below.", "url": "https://www.rcsb.org/docs/programmatic-access/web-apis-overview", "snapshot_id": "s03", "char_start": 10636, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } ], "terms": { "same_as_card_license": false, "own_terms": { "commercial_use": "conditional", "redistribution": "conditional", "evidence": [ { "location": "terms-page", "excerpt": "Data provided by RCSB PDB programmatic APIs are available under the same license unless they originate from an integrated external resource , in which case the licensing restrictions applied by the data provider must be followed.", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02", "char_start": 9042, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] } }, "reachable": { "status": 200, "checked_on": "2026-11-14" } }, { "method": "bulk-download", "url": "https://files.wwpdb.org", "formats": [ "PDBx/mmCIF", "XML", "PDB" ], "limits": [ { "text": { "en": "The FTP file download protocol in the PDB archive has been deprecated since November 1st 2024.", "zh": "PDB档案中的FTP文件下载协议自2024年11月1日起已被弃用。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Please note that the FTP file download protocol in the PDB archive has been deprecated since November 1st 2024 ( announcement ).", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites", "snapshot_id": "s06", "char_start": 1114, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } ], "terms": { "same_as_card_license": true, "own_terms": null }, "reachable": { "status": 200, "checked_on": "2026-11-14" } }, { "method": "web-api", "url": "https://www.rcsb.org/docs/programmatic-access/file-download-services", "formats": [], "limits": [], "terms": { "same_as_card_license": true, "own_terms": null }, "statement": { "text": { "en": "Bulk archive download is by HTTPS (files.wwpdb.org) or rsync; FTP is no longer supported. The archive is also on the AWS Registry of Open Data.", "zh": "整库下载走 HTTPS（files.wwpdb.org）或 rsync，FTP 已不再支持；归档也托管在 AWS 开放数据登记处。" }, "evidence": [ { "location": "dataset-page", "excerpt": "All data are available via the HTTPS protocol. Note that the FTP protocol is no longer supported.", "url": "https://www.rcsb.org/docs/programmatic-access/file-download-services", "snapshot_id": "s09", "char_start": 6392, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "File Download Services", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/docs/programmatic-access/file-download-services" } } ] }, "reachable": { "status": 200, "checked_on": "2026-11-14" } } ], "versioning": { "latest": null, "update_cycle": { "cycle": "weekly", "statement": { "text": { "en": "The PDB archive and versioned archive are updated every Wednesday at 00:00 UTC.", "zh": "PDB档案和版本化档案每周三00:00 UTC更新。" }, "evidence": [ { "location": "dataset-page", "excerpt": "The PDB archive and versioned archive are updated every Wednesday at 00:00 UTC.", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites", "snapshot_id": "s06", "char_start": 1244, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } }, "breaking_changes": [ { "version": "12-character PDB ID DOI format", "date": "2027-07-21", "kind": "identifier", "statement": { "text": { "en": "PDB entries deposited on or after July 21, 2027 will use the 12-character PDB ID DOI format 10.2210/pdb_1000axyz/pdb.", "zh": "2027年7月21日及以后存缴的PDB条目将使用12字符PDB ID的DOI格式10.2210/pdb_1000axyz/pdb。" }, "evidence": [ { "location": "terms-page", "excerpt": "PDB entries deposited on or after July 21, 2027 , will use the 12-character PDB ID DOI format 10.2210/pdb_1000axyz/pdb (where pdb_1000axyz is the 12-character PDB ID).", "url": "https://www.rcsb.org/pages/policies", "snapshot_id": "s02", "char_start": 3273, "verified_on": "2026-11-12", "observed": "page", "captured_by": "pipeline" } ] } }, { "version": "December 9", "date": "2020-12-03", "kind": "content-removed", "statement": { "text": { "en": "The legacy RCSB REST search and fetch APIs were shut down on 9 December 2020 in favour of the Search and Data APIs.", "zh": "RCSB 旧版 REST 检索与获取接口于 2020-12-09 下线，由 Search API 与 Data API 取代。" }, "evidence": [ { "location": "official-change-notice", "excerpt": "legacy RCSB PDB APIs (REST search and fetch) will be discontinued on December 9, 2020 as announced previously.", "url": "https://www.rcsb.org/news/5fc9176809ae2a096d081e28", "snapshot_id": "s13", "char_start": 2506, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Legacy API Shutdown December 9", "authors_or_org": "RCSB Protein Data Bank", "date": "2020-12-03", "date_as_written": "2020-12-03", "source_type": "official-change-notice", "open_access": true, "doi_or_url": "https://www.rcsb.org/news/5fc9176809ae2a096d081e28" } } ] } }, { "version": " 2024", "date": "2024-09-18", "kind": "format", "statement": { "text": { "en": "wwPDB deprecated the FTP download protocol on 1 November 2024; HTTPS and rsync remain.", "zh": "wwPDB 于 2024-11-01 停用 FTP 下载协议，保留 HTTPS 与 rsync。" }, "evidence": [ { "location": "official-change-notice", "excerpt": "wwPDB plans to deprecate FTP download protocol on November 1st 2024", "url": "https://pdbj.org/news/Deprecation_FTP_Nov2024", "snapshot_id": "s14", "char_start": 709, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024", "authors_or_org": "wwPDB (posted by PDBj)", "date": "2024-09-18", "date_as_written": "2024-09-18", "source_type": "official-change-notice", "open_access": true, "doi_or_url": "https://pdbj.org/news/Deprecation_FTP_Nov2024" } } ] } }, { "version": "62", "date": null, "kind": "identifier", "statement": { "text": { "en": "Large structures that used to be split across several PDB-format files were merged into single entries at the end of 2014.", "zh": "过去被拆成多个 PDB 格式文件的大结构已于 2014 年底合并为单一条目。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Historically, large files containing >62 chains and/or 99999 ATOM lines were \"split\" across multiple PDB format files. These files were combined into single entries at the end of 2014", "url": "https://www.rcsb.org/docs/general-help/structures-without-legacy-pdb-format-files", "snapshot_id": "s15", "char_start": 5977, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Structures Without Legacy PDB Format Files", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/docs/general-help/structures-without-legacy-pdb-format-files" } } ] } } ], "history_url": null, "notes": [ { "text": { "en": "New and modified PDB entries are released weekly; files are updated at the wwPDB sites every Wednesday from 00:00 UTC.", "zh": "PDB 按周发布：每周三 00:00 UTC 起各 wwPDB 站点更新全部新增与修改条目。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Phase II: Every Wednesday from 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB FTP sites.", "url": "https://www.wwpdb.org/documentation/policy", "snapshot_id": "s07", "char_start": 25518, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "wwPDB Deposition Policies and wwPDB Biocuration Procedures, Section A", "authors_or_org": "wwPDB annotation staff", "date": "2026-10", "date_as_written": "2026-10 (version 5.6)", "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.wwpdb.org/documentation/policy" } } ] }, { "text": { "en": "The PDB has no numbered data release; the '5.6' label belongs to the deposition-policy document, not to the data (the policy change log lists it as a document revision).", "zh": "PDB 数据本身没有编号版本；“5.6”是收存政策文档的版本号，不是数据版本（政策变更日志把它列为文档修订）。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Version 5.6 (October 2026): Updated change log to provide a complete record of change history.", "url": "https://www.wwpdb.org/documentation/policy", "snapshot_id": "s07", "char_start": 4837, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "wwPDB Deposition Policies and wwPDB Biocuration Procedures, Section A", "authors_or_org": "wwPDB annotation staff", "date": "2026-10", "date_as_written": "2026-10", "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.wwpdb.org/documentation/policy" } } ] }, { "text": { "en": "On the check date the RCSB home page counted 262,786 experimental structures, 410 integrative structures and 1,062,058 computed structure models.", "zh": "查证当日 RCSB 首页显示实验结构 262,786 个、整合结构 410 个、计算结构模型 1,062,058 个。" }, "evidence": [ { "location": "dataset-page", "excerpt": "262,786 Experimental Structures 410 Integrative Structures Computed Structure Models (CSM): 1,062,058 From AlphaFoldDB and ModelArchive", "url": "https://www.rcsb.org/", "snapshot_id": "s21", "char_start": null, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "RCSB PDB: Homepage", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/" } } ] }, { "text": { "en": "Besides the main archive, wwPDB runs a versioned archive and, since 1 February 2023, a 'NextGen' archive carrying the latest entry versions enriched with extra annotation.", "zh": "除主归档外，wwPDB 还提供版本化归档；自 2023-02-01 起另有 NextGen 归档，分发附加注释的各条目最新版本。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Since February 01 2023, the wwPDB enriches PDB entries with additional annotation and distributes the latest versions of each entry via next generation archive (NextGen) accessible at files-nextgen.wwpdb.org .", "url": "https://www.rcsb.org/docs/programmatic-access/file-download-services", "snapshot_id": "s09", "char_start": 5927, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "File Download Services", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/docs/programmatic-access/file-download-services" } } ] } ] }, "known_defects": [ { "kind": "data-quality", "statement": { "text": { "en": "The page states that structures determined before experimental data deposition became mandatory may have no available experimental data, and that such structures are difficult to validate without it.", "zh": "该页面指出，在实验数据存缴成为强制要求之前确定的结构可能已无实验数据，而缺少实验数据时难以验证这些结构。" }, "evidence": [ { "location": "terms-page", "excerpt": "On occasion, the wwPDB is asked to archive a structure that was determined before deposition of experimental data became mandatory and the experimental data are no longer available. It is difficult to validate such structures without experimental data.", "url": "https://www.wwpdb.org/documentation/policy", "snapshot_id": "s05", "char_start": 6240, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] }, "source_kind": "official-note", "scope": "PDB entries determined before mandatory experimental data deposition", "attribution": { "who": "wwpdb.org", "when": "2026-11-13", "source_type": "official-page", "title": null }, "correction_entrance": "Report an error through the publisher: https://www.rcsb.org/" }, { "kind": "other", "statement": { "text": { "en": "RCSB: X-ray ligands without deposited structure factors (typically before 2008) cannot be checked for fit to experimental data.", "zh": "RCSB 说明：没有提交结构因子的 X 射线结构（多为 2008 年前）无法评估配体与实验数据的吻合度。" }, "evidence": [ { "location": "dataset-page", "excerpt": "ligands in X-ray structures lacking associated structure factor data (typically deposited prior to 2008), as goodness-of-fit to the experimental data cannot be calculated without structure factor data.", "url": "https://www.rcsb.org/docs/general-help/ligand-structure-quality-in-pdb-structures", "snapshot_id": "s16", "char_start": 8342, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Ligand Structure Quality in PDB Structures", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/docs/general-help/ligand-structure-quality-in-pdb-structures" } } ] }, "source_kind": "official-note", "scope": null, "attribution": { "who": "RCSB Protein Data Bank", "when": "date not stated (page read 2026-11-13)", "source_type": "official-page", "title": "Ligand Structure Quality in PDB Structures" }, "correction_entrance": "Report an error through the publisher or the authors: https://www.rcsb.org/docs/general-help/ligand-structure-quality-in-pdb-structures" }, { "kind": "identifier", "statement": { "text": { "en": "wwPDB: when experimental data change, a new entry with a new ID replaces the old one, which is obsoleted but stays in the archive.", "zh": "wwPDB 说明：实验数据变更须以新 ID 新条目替代，旧条目被废止但仍留在归档中。" }, "evidence": [ { "location": "dataset-page", "excerpt": "The old entry is then obsoleted (if the depositor wishes) and replaced (superseded) by the new one.", "url": "https://www.wwpdb.org/documentation/policy", "snapshot_id": "s07", "char_start": 29326, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "wwPDB Deposition Policies and wwPDB Biocuration Procedures, Section A", "authors_or_org": "wwPDB annotation staff", "date": "2026-10", "date_as_written": "2026-10 (version 5.6)", "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.wwpdb.org/documentation/policy" } } ] }, "source_kind": "official-note", "scope": null, "attribution": { "who": "wwPDB annotation staff", "when": "2026-10", "source_type": "official-page", "title": "wwPDB Deposition Policies and wwPDB Biocuration Procedures, Section A" }, "correction_entrance": "Report an error through the publisher or the authors: https://www.wwpdb.org/documentation/policy" }, { "kind": "other", "statement": { "text": { "en": "Buttenschoen, Morris and Deane (PoseBusters) report that deep-learning docking methods trained on PDB-derived sets often produce physically implausible poses, and that RMSD alone is not a sufficient evaluation.", "zh": "Buttenschoen、Morris、Deane（PoseBusters）报告：基于 PDB 衍生数据训练的深度学习对接方法常产出物理上不合理的构象，只看 RMSD 不足以评估。" }, "evidence": [ { "location": "peer-reviewed-paper", "excerpt": "It is therefore not sufficient to evaluate these methods solely by RMSD to a native binding mode.", "url": "https://europepmc.org/article/MED/38425520", "snapshot_id": "s22", "char_start": 390, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences", "authors_or_org": "Buttenschoen M, Morris GM, Deane CM (Chemical Science)", "date": "2023-12-13", "date_as_written": "2023-12-13", "source_type": "peer-reviewed-paper", "open_access": true, "doi_or_url": "https://europepmc.org/article/MED/38425520" } } ] }, "source_kind": "peer-reviewed-paper", "scope": null, "attribution": { "who": "Buttenschoen M, Morris GM, Deane CM (Chemical Science)", "when": "2023-12-13", "source_type": "peer-reviewed-paper", "title": "PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences" }, "correction_entrance": "Report an error through the publisher or the authors: https://europepmc.org/article/MED/38425520" } ], "fit": { "suited_for": [ { "text": { "en": "The page states that annual archive snapshots may be used to provide a stable set of entries for analysis and to show changes introduced by wwPDB remediation efforts.", "zh": "该页面指出，年度档案快照可用于提供稳定的条目集合以供分析，并显示wwPDB修复工作带来的变化。" }, "evidence": [ { "location": "dataset-page", "excerpt": "The annual archive snapshots provide the data in the archive at the start of each year or at selected milestone moments. These data may be used to provide a stable set of entries for analysis and allow users to see changes introduced due to remediation efforts by wwPDB.", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites", "snapshot_id": "s06", "char_start": 11854, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] }, { "text": { "en": "RCSB states that computed structure models can serve as starting models for proteins and complexes whose structures have not been determined experimentally.", "zh": "RCSB 说明：对尚无实验结构的蛋白及复合物，计算结构模型可作起始模型。" }, "evidence": [ { "location": "dataset-page", "excerpt": "Yet CSMs can provide great starting models for the millions of proteins and their complexes whose structures have not been experimentally determined.", "url": "https://www.rcsb.org/docs/general-help/computed-structure-models-and-rcsborg", "snapshot_id": "s17", "char_start": 8073, "verified_on": "2026-11-13", "observed": "page", "source_work": { "title": "Computed Structure Models and RCSB.org", "authors_or_org": "RCSB Protein Data Bank", "date": null, "date_as_written": null, "source_type": "official-page", "open_access": true, "doi_or_url": "https://www.rcsb.org/docs/general-help/computed-structure-models-and-rcsborg" } } ] } ], "not_suited_for": [ { "text": { "en": "Theoretical model depositions determined purely in silico, for example by homology or ab initio methods, are no longer accepted.", "zh": "完全在计算机中确定的纯理论模型存缴（例如通过同源建模或从头计算方法）已不再被接受。" }, "evidence": [ { "location": "terms-page", "excerpt": "Theoretical model depositions determined purely in silico using, for example, homology or ab initio methods, are no longer accepted.", "url": "https://www.wwpdb.org/documentation/policy", "snapshot_id": "s05", "char_start": 10254, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] }, { "text": { "en": "The page directs that crystal structures of peptides with fewer than 24 residues within any polymer chain that do not meet the stated criteria be deposited at the Cambridge Crystallographic Data Centre.", "zh": "该页面要求，任何聚合物链中残基少于24个且不符合所述标准的肽晶体结构应存缴至剑桥晶体学数据中心。" }, "evidence": [ { "location": "terms-page", "excerpt": "Crystal structures of peptides with fewer than 24 residues within any polymer chain that do not meet the criteria above should be deposited at the Cambridge Crystallographic Data Centre", "url": "https://www.wwpdb.org/documentation/policy", "snapshot_id": "s05", "char_start": 13368, "verified_on": "2026-11-13", "observed": "page", "captured_by": "pipeline" } ] } ] }, "commercial_access": { "route": "unknown", "url": null, "statement": null }, "completeness": { "core_complete": false, "literature_defects": 1, "reachable_access": 3, "meets_practical_bar": false, "gaps": [ { "field": "versioning.latest", "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": [ { "name": "Atomic coordinates", "url": "https://files.wwpdb.org/pub/pdb/data/structures/", "size_text": null, "checksum": null, "format": "PDBx/mmCIF, XML, and PDB", "version": null, "evidence": { "excerpt": "Atomic coordinates PDBx/mmCIF, XML, and PDB https://files.wwpdb.org/pub/pdb/data/structures/", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "X-ray data: Structure Factors", "url": "https://files.wwpdb.org/pub/pdb/data/structures/divided/structure_factors/", "size_text": null, "checksum": null, "format": "PDBx/mmCIF", "version": null, "evidence": { "excerpt": "X-ray data: Structure Factors PDBx/mmCIF https://files.wwpdb.org/pub/pdb/data/structures/divided/structure_factors/", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "NMR data: Restraints and chemical shifts", "url": "https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/", "size_text": null, "checksum": null, "format": "NEF (/nmr_data), NMR-STAR, and native refinement program formats", "version": null, "evidence": { "excerpt": "NMR data: Restraints and chemical shifts NEF (/nmr_data), NMR-STAR, and native refinement program formats https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "NMR chemical shifts", "url": "https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_chemical_shifts/", "size_text": null, "checksum": null, "format": "NEF (/nmr_data), NMR-STAR, and native refinement program formats", "version": null, "evidence": { "excerpt": "https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_chemical_shifts/", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "Small molecules references: CCD", "url": "https://files.wwpdb.org/pub/pdb/refdata/chem_comp/", "size_text": null, "checksum": null, "format": "PDBx/mmCIF", "version": null, "evidence": { "excerpt": "Small molecules references: CCD and BIRD PDBx/mmCIF https://files.wwpdb.org/pub/pdb/refdata/chem_comp/ https://files.wwpdb.org/pub/pdb/refdata/bird", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "Small molecules references: BIRD", "url": "https://files.wwpdb.org/pub/pdb/refdata/bird", "size_text": null, "checksum": null, "format": "PDBx/mmCIF", "version": null, "evidence": { "excerpt": "https://files.wwpdb.org/pub/pdb/refdata/bird", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "Assemblies (mmCIF)", "url": "https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/", "size_text": null, "checksum": null, "format": "PDBx/mmCIF, PDB", "version": null, "evidence": { "excerpt": "Assemblies PDBx/mmCIF, PDB https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/ https://files.wwpdb.org/pub/pdb/data/biounit/PDB/", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "Assemblies (PDB)", "url": "https://files.wwpdb.org/pub/pdb/data/biounit/PDB/", "size_text": null, "checksum": null, "format": "PDBx/mmCIF, PDB", "version": null, "evidence": { "excerpt": "https://files.wwpdb.org/pub/pdb/data/biounit/PDB/", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "Archive holdings", "url": "https://files.wwpdb.org/pub/pdb/holdings/", "size_text": null, "checksum": null, "format": "JSON", "version": null, "evidence": { "excerpt": "Archive holdings JSON https://files.wwpdb.org/pub/pdb/holdings/", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "RCSB PDB coordinate files in PDB Exchange Format (mmCIF)", "url": "https://files.rcsb.org/pub/pdb/data/structures/divided/mmCIF", "size_text": null, "checksum": null, "format": "PDB Exchange Format (mmCIF)", "version": null, "evidence": { "excerpt": "Download coordinate files in PDB Exchange Format (mmCIF): https://files.rcsb.org/pub/pdb/data/structures/divided/mmCIF", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "RCSB PDB coordinate files in PDBML format", "url": "https://files.rcsb.org/pub/pdb/data/structures/divided/XML", "size_text": null, "checksum": null, "format": "PDBML (XML)", "version": null, "evidence": { "excerpt": "Download coordinate files in PDBML format: https://files.rcsb.org/pub/pdb/data/structures/divided/XML", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "name": "RCSB PDB coordinate files in PDB format", "url": "https://files.rcsb.org/pub/pdb/data/structures/divided/pdb", "size_text": null, "checksum": null, "format": "PDB", "version": null, "evidence": { "excerpt": "Download coordinate files in PDB format: https://files.rcsb.org/pub/pdb/data/structures/divided/pdb", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } } ], "api": [], "registration": null, "bulk_download": [ { "command_text": "rsync -rlpt -v -z --delete --port=33444 \\ rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ ./mmCIF", "evidence": { "excerpt": "Download coordinate files in PDB Exchange Format (mmCIF): rsync -rlpt -v -z --delete --port=33444 \\ rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ ./mmCIF", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "command_text": "rsync -rlpt -v -z --delete --port=33444 \\ rsync.rcsb.org::ftp_data/structures/divided/XML/ ./XML", "evidence": { "excerpt": "Download coordinate files in PDBML Format (xml): rsync -rlpt -v -z --delete --port=33444 \\ rsync.rcsb.org::ftp_data/structures/divided/XML/ ./XML", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "command_text": "rsync -rlpt -v -z --delete --port=33444 \\ rsync.rcsb.org::ftp_data/structures/divided/pdb/ ./pdb", "evidence": { "excerpt": "Download coordinate files in PDB Format: rsync -rlpt -v -z --delete --port=33444 \\ rsync.rcsb.org::ftp_data/structures/divided/pdb/ ./pdb", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "command_text": "rsync -rlpt -v -z --delete --port=33444 \\ rsync.rcsb.org::ftp/validation_reports/ ./validation_reports", "evidence": { "excerpt": "Download the validation report files: rsync -rlpt -v -z --delete --port=33444 \\ rsync.rcsb.org::ftp/validation_reports/ ./validation_reports", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "command_text": "aws s3 sync s3://pdbsnapshots/ ./local-directory/ --no-sign-request", "evidence": { "excerpt": "All PDB Snapshot objects aws s3 sync s3://pdbsnapshots/ ./local-directory/ --no-sign-request", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } }, { "command_text": "aws s3 sync s3://pdbsnapshots/20250101/ ./local-directory/20250101 --no-sign-request", "evidence": { "excerpt": "Specific PDB snapshot object (e.g., /20250101) aws s3 sync s3://pdbsnapshots/20250101/ ./local-directory/20250101 --no-sign-request", "snapshot_id": "s06", "url": "https://www.wwpdb.org/ftp/pdb-ftp-sites" } } ], "gaps": [ "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: AlphaFold Protein Structure Database (https://mdexa.com/datasets/alphafold-db/); GEO (https://mdexa.com/datasets/geo/); gnomAD (https://mdexa.com/datasets/gnomad/).", "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": "AlphaFold Protein Structure Database", "url": "https://mdexa.com/datasets/alphafold-db/", "json": "https://mdexa.com/datasets/alphafold-db.json" }, { "name": "GEO", "url": "https://mdexa.com/datasets/geo/", "json": "https://mdexa.com/datasets/geo.json" }, { "name": "gnomAD", "url": "https://mdexa.com/datasets/gnomad/", "json": "https://mdexa.com/datasets/gnomad.json" } ] } }