Taylor Scott
Citing the Protein Data Bank (PDB) is essential for acknowledging the use of structural data in scientific research. The PDB, a global repository of 3D protein and nucleic acid structures, provides unique identifiers for each entry, which should be included in citations. Proper citation ensures credit to the original researchers and facilitates reproducibility. To cite a PDB entry, include the PDB ID (e.g., 1CRN), the title of the structure, authors, journal reference, and the PDB website URL. Additionally, follow specific guidelines from journals or style manuals, such as APA or MLA, to format the citation correctly. Accurate citation practices uphold academic integrity and support the continued growth of the PDB as a vital resource in structural biology.
| Characteristics | Values |
|---|---|
| Citation Format | Authors. (Year). Title of the structure. Protein Data Bank, PDB ID. doi:10.2210/[PDB ID] |
| Example Citation | Smith, J., & Doe, A. (2023). Crystal structure of human hemoglobin. Protein Data Bank, 1HHO. doi:10.2210/1HHO |
| PDB ID Format | 4-character alphanumeric code (e.g., 1HHO, 6ZUE) |
| DOI Prefix | 10.2210/ |
| Citation Style | Varies (APA, MLA, Chicago, etc.), but follows general format above |
| Acknowledgment | Recommended to acknowledge PDB (e.g., "Structural data were obtained from the Protein Data Bank (PDB ID: 1HHO)") |
| PDB Website | www.rcsb.org |
| Citation Generator | Available on PDB website for specific structures |
| Versioning | Not applicable (PDB IDs are unique and do not change) |
| Access Date | Optional, but recommended for online resources (e.g., "Retrieved from www.rcsb.org on [Date]") |
| License | PDB data are freely available under the PDB License Agreement |
| Reference List Entry | Smith, J., & Doe, A. (2023). Crystal structure of human hemoglobin. Protein Data Bank, 1HHO. doi:10.2210/1HHO |
| In-Text Citation | (Smith & Doe, 2023) or ...as shown in the structure (PDB ID: 1HHO) |
| PDB Format | PDB, mmCIF, or other supported formats |
| Metadata | Experimental details, authors, and publication information available on PDB website |
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What You'll Learn
- PDB Format Overview: Understand the structure and content of PDB files for accurate citation
- Accession Codes: Use unique 4-character codes to identify and cite specific PDB entries
- Citation Guidelines: Follow official PDB recommendations for proper academic referencing in publications
- Software Tools: Utilize tools like RCSB PDB for generating correct citation formats
- Version Control: Cite specific PDB file versions to ensure reproducibility in research
PDB Format Overview: Understand the structure and content of PDB files for accurate citation
The Protein Data Bank (PDB) format is a critical resource for structural biologists, providing detailed atomic coordinates and metadata for biomolecules. Understanding the structure and content of PDB files is essential for accurate citation, ensuring that researchers properly acknowledge the source of structural data. A PDB file is a text-based format that contains a wealth of information, including atomic coordinates, connectivity, and experimental metadata. The file is divided into several sections, each serving a specific purpose. The primary sections include the header, title, compound, source, and coordinate sections, among others. Familiarizing oneself with these sections is the first step toward accurate citation, as it allows researchers to extract the necessary details for proper attribution.
The header section of a PDB file, denoted by the `HEADER` record, provides essential metadata such as the PDB ID, deposition date, and classification of the biomolecule. This section is crucial for citation, as it contains the unique identifier (PDB ID) that distinguishes each structure in the database. Additionally, the title section (`TITLE` record) offers a brief description of the biomolecule, which can be useful for context in citations. The compound and source sections (`COMPND` and `SOURCE` records) provide details about the molecule’s composition and biological source, respectively. These sections are valuable for ensuring that citations accurately reflect the nature and origin of the structural data.
The coordinate section (`ATOM` and `HETATM` records) is the core of the PDB file, containing the 3D atomic coordinates of the biomolecule. While this section is not directly used for citation, understanding its structure is important for comprehending the data being referenced. Other sections, such as `EXPDTA` (experimental data) and `REMARK` (additional comments), provide insights into the methods used to determine the structure and any relevant notes from the depositors. These details can enhance the accuracy and completeness of citations by providing context about the experimental techniques employed.
For accurate citation, researchers should focus on key elements extracted from the PDB file. The PDB ID, found in the header section, is the most critical piece of information, as it uniquely identifies the structure. The title and compound sections can provide additional context, such as the common name of the biomolecule or its biological function. When citing a PDB entry, the recommended format typically includes the authors (if available), the year of data release, the PDB ID, and the title of the structure. For example: "Smith et al. (2020) Protein kinase A (PDB ID: 1ATP)."
In addition to the PDB file itself, researchers should consult external resources provided by the Protein Data Bank, such as the PDB entry page, which offers a summary of the structure and citation guidelines. The PDB also provides a standardized citation format, which often includes a DOI (Digital Object Identifier) for the entry. Using the DOI ensures that the citation is linked to the most up-to-date version of the data. By combining information from the PDB file with these external resources, researchers can create accurate, comprehensive, and properly formatted citations that adhere to academic and scientific standards.
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Accession Codes: Use unique 4-character codes to identify and cite specific PDB entries
When citing specific Protein Data Bank (PDB) entries, the use of accession codes is essential. These codes are unique, 4-character identifiers assigned to each structure deposited in the PDB. For example, the structure of hemoglobin is identified by the code 1GZX. This code serves as a direct and unambiguous reference to the specific dataset, ensuring clarity and precision in scientific communication. Always include the accession code in your citation to allow readers to locate the exact structure you are referencing.
To properly cite a PDB entry using its accession code, follow a standardized format. Begin with the words "Protein Data Bank" or the abbreviation "PDB," followed by the accession code in parentheses. For instance, a citation would read: "Protein Data Bank (1GZX)." This format is widely recognized in the scientific community and ensures consistency across publications. If you are citing multiple structures, list each accession code separately, such as "PDB (1GZX, 2HHB)." This approach simplifies the process for both authors and readers.
In addition to the accession code, it is good practice to include the year of deposition or the version of the structure if relevant. For example, you might write: "Protein Data Bank (1GZX, 2003)." This provides additional context, especially if the structure has been updated or revised over time. However, the accession code remains the primary identifier and should always be the focal point of the citation. Including the DOI (Digital Object Identifier) for the PDB entry, if available, can further enhance the citation's completeness.
When integrating PDB accession codes into your text, ensure they are clearly distinguished from the surrounding content. Use bold or italics for the code, such as 1GZX, to make it stand out. Avoid embedding the code within a long sentence where it might be overlooked. Instead, place it in a prominent position, such as at the beginning or end of a sentence, to ensure it is easily identifiable. This practice aligns with best practices for scientific writing and data citation.
Finally, always verify the accession code for accuracy before finalizing your citation. The PDB website (https://www.rcsb.org) provides a search function to confirm the correct code and retrieve additional details about the structure. Mistyping or misidentifying the code can lead to confusion or incorrect referencing. By using the correct accession code and following these guidelines, you ensure that your citations are both precise and professional, contributing to the reliability of your work.
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Citation Guidelines: Follow official PDB recommendations for proper academic referencing in publications
When citing the Protein Data Bank (PDB) in academic publications, it is essential to follow the official recommendations provided by the PDB to ensure proper attribution and compliance with academic standards. The PDB is a critical resource for structural biology, and accurate citation helps acknowledge the contributions of depositors and maintainers of the database. The PDB provides clear guidelines on how to cite both the PDB itself and the specific structures accessed from it. These guidelines emphasize the importance of recognizing the original depositors of the structural data, as well as the PDB as the repository.
The primary recommendation for citing the PDB in general terms is to reference the PDB archive as a whole. The suggested citation format includes the name of the database, its accession year, and the URL. For example, a citation might read: "Protein Data Bank, 2023. [https://www.rcsb.org]" (RCSB Protein Data Bank, 2023). This format ensures that readers can easily locate the resource and acknowledges the ongoing efforts of the PDB in maintaining and updating the database. It is also important to include the specific PDB ID(s) of the structures used in your research, as this directly credits the original contributors of the structural data.
When citing individual PDB entries, the official guidelines stress the need to include the PDB ID, the title of the structure, the authors of the original publication, the journal reference, and the DOI (if available). For instance, a citation could be formatted as: "Smith J, Doe A, et al. (2022). Crystal Structure of Example Protein. *Journal of Structural Biology*, 300(2), 123456. [DOI: 10.1016/j.jsb.2022.123456] (PDB ID: 1ABC)." This detailed citation ensures that both the original researchers and the PDB are appropriately acknowledged. Including the DOI facilitates easy access to the original publication for readers.
In addition to these specifics, the PDB recommends acknowledging the funding bodies and organizations that support the PDB archive. For example, the RCSB Protein Data Bank is primarily funded by the National Science Foundation, the National Institute of General Medical Sciences, and the U.S. Department of Energy. Including such acknowledgments in the "Acknowledgments" or "Funding" section of your publication highlights the collaborative nature of scientific research and the infrastructure that enables it. This practice aligns with ethical academic standards and fosters transparency in research.
Finally, for software tools or web services that utilize PDB data, the guidelines advise citing both the specific tool and the PDB itself. For example, if using the PDB's web-based visualization tool, include a citation for the tool along with the general PDB citation. This ensures that all contributors to the research process, from data depositors to software developers, receive appropriate credit. Adhering to these citation guidelines not only upholds academic integrity but also supports the sustainability of the PDB as a vital resource for the scientific community. Always consult the PDB's official citation guide for the most up-to-date recommendations.
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Software Tools: Utilize tools like RCSB PDB for generating correct citation formats
When citing structures from the Protein Data Bank (PDB), accuracy and consistency are crucial. The RCSB PDB website (www.rcsb.org) offers built-in tools to generate correct citation formats, ensuring compliance with academic and scientific standards. To begin, navigate to the RCSB PDB homepage and search for the specific PDB entry you wish to cite. Once you access the entry’s page, look for the "Cite This Entry" or "Citation" section, typically located in the header or sidebar. This feature automatically generates a citation in the recommended format, which includes essential details such as the PDB ID, authors, title, journal reference, and DOI. Using this tool eliminates the risk of errors and ensures the citation is up-to-date.
Another useful feature of the RCSB PDB is its ability to export citations in multiple formats, such as APA, MLA, Chicago, and BibTeX. To access this, click on the "Download Files" or "Export" option on the PDB entry page and select the citation format you require. This is particularly helpful for researchers using reference management software like Zotero, Mendeley, or EndNote, as it allows seamless integration of PDB citations into larger bibliographies. The RCSB PDB also provides a suggested citation format for cases where the structure is used in publications, presentations, or educational materials, ensuring proper acknowledgment of the data contributors.
For users who prefer programmatic access, the RCSB PDB API offers endpoints to retrieve citation information directly. By querying the API with a specific PDB ID, developers can obtain structured citation data in JSON or XML format, which can then be formatted according to their needs. This is especially useful for bioinformatics tools, databases, or applications that require automated citation generation. Documentation for the API is available on the RCSB PDB website, providing clear instructions on how to implement this functionality.
In addition to the RCSB PDB, other software tools like PDBj (Protein Data Bank Japan) and PDBe (Protein Data Bank in Europe) also provide citation generation features. These tools often include region-specific or specialized citation formats, catering to diverse user needs. However, the RCSB PDB remains the most widely used resource due to its comprehensive database and user-friendly interface. Regardless of the tool chosen, always verify the generated citation against the original publication to ensure accuracy, as minor discrepancies may occasionally occur.
Lastly, it is important to note that citing PDB entries is not just a formality but a critical aspect of scientific integrity. Proper citation acknowledges the efforts of structural biologists and ensures traceability of data. By utilizing software tools like the RCSB PDB, researchers can streamline the citation process, save time, and focus on their core work. Whether you are a student, educator, or professional researcher, leveraging these tools will help you maintain high standards in your scientific communications.
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Version Control: Cite specific PDB file versions to ensure reproducibility in research
When citing Protein Data Bank (PDB) files in research, version control is essential to ensure reproducibility and transparency. The PDB archive frequently updates entries with revised coordinates, improved annotations, or corrected metadata. As a result, citing a specific version of a PDB file is critical to guarantee that other researchers can access the exact dataset used in your study. Each PDB entry is assigned a unique four-character code (e.g., 1AK4), but this alone does not specify the version. To cite a particular version, include the release date or the PDB’s "deposition date" alongside the PDB ID. This information can be found in the PDB entry’s header or on the PDB website under the entry’s revision history.
To implement version control effectively, researchers should familiarize themselves with the PDB’s versioning system. Each update to a PDB entry is documented, and the release date serves as a version identifier. For example, if you used the structure of a protein from PDB ID 1AK4 in your research, and the specific version you accessed was released on January 1, 2020, your citation should reflect this: "PDB ID 1AK4 (released January 1, 2020)." This practice ensures that anyone attempting to replicate your work can retrieve the same structural data, even if the entry is updated in the future.
In addition to the release date, researchers can use the PDB’s "revision number" or "status" field for more precise version control. The status field indicates whether the entry is "obsolete," "replaced," or "current," providing further context about the version used. Including this information in citations enhances clarity and reproducibility. For instance, a citation could read: "PDB ID 1AK4, revision 2, released January 1, 2020." Tools like the PDB’s REST API or the `pdb-tools` command-line utility can assist in retrieving version-specific metadata programmatically, streamlining the process for researchers.
Proper citation of PDB file versions is not only a best practice but also aligns with the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. By explicitly stating the version, researchers contribute to a more transparent and reproducible scientific ecosystem. Journals and funding agencies increasingly require detailed citations of datasets, including structural data from the PDB. Therefore, incorporating version control into your citation workflow is a proactive step toward meeting these standards and ensuring the longevity of your research.
Finally, when citing PDB files in publications, follow established guidelines such as those from the International Committee of Medical Journal Editors (ICMJE) or discipline-specific style guides (e.g., APA, MLA). Include the PDB ID, version identifier (release date or revision number), and a DOI if available. For example: "The structure was retrieved from the Protein Data Bank (PDB ID 1AK4, released January 1, 2020; DOI: 10.2210/pdb1AK4/pdb)." This comprehensive approach to citation not only ensures reproducibility but also acknowledges the ongoing efforts of the PDB archive in maintaining and updating structural data for the scientific community.
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Frequently asked questions
To cite a PDB entry, use the following format: "Protein Data Bank (PDB) entry [PDB ID] (doi:10.2210/[PDB ID])". For example, for PDB ID 1CRN, the citation would be: "Protein Data Bank (PDB) entry 1CRN (doi:10.2210/1CRN)".
The DOI for a PDB entry is available on the PDB website. Visit the entry’s page, and the DOI will be listed under the "Citation" section. Alternatively, the DOI can be constructed using the format "doi:10.2210/[PDB ID]".
While the PDB ID and DOI are sufficient for citing the structure, it is good practice to also acknowledge the original authors of the structure in your reference list. Include the publication associated with the PDB entry, if available, in addition to the PDB citation.
