Megan Brooks
The RCSB Protein Data Bank (PDB) is a vital resource for researchers, providing access to 3D structures of proteins, nucleic acids, and other biomolecules. Properly citing the PDB is essential for acknowledging the work of contributors and ensuring academic integrity. When citing the RCSB PDB, include the PDB ID (e.g., 1CRN), the title of the entry, the authors, the journal reference, and the DOI or URL. For example, a citation might appear as: Berman, H.M., et al. (2000) The Protein Data Bank. Nucleic Acids Research 28: 235-242. DOI: 10.1093/nar/28.1.235. PDB ID: 1CRN. Additionally, the RCSB PDB website offers specific citation guidelines and tools to help users generate accurate references, ensuring proper attribution in scientific publications and presentations.
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What You'll Learn
PDB Format Citation Guidelines
When citing the RCSB Protein Data Bank (PDB) in the context of PDB format, it is essential to follow specific guidelines to ensure proper acknowledgment of the resource. The PDB format is a standard file format used to describe the three-dimensional structures of proteins, nucleic acids, and other molecules. To cite a PDB file or the PDB database in general, start by identifying the specific PDB entry or entries you are referencing. Each PDB entry has a unique 4-character identifier (e.g., 1CRN), which should be included in your citation. The RCSB PDB recommends using the following format for citing individual PDB entries: "PDB ID: [PDB entry ID]; [Author(s) of the structure]; [Year of deposition]; [Title of the structure]." For example, "PDB ID: 1CRN; Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.; 2000; The Protein Data Bank."
In addition to citing individual PDB entries, you may also need to cite the PDB database as a whole. In this case, the RCSB PDB provides a general citation format that acknowledges the resource and its contributors. The recommended citation for the PDB database is: "Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Research, 28, 235-242." This citation should be used when referencing the PDB as a comprehensive resource, rather than specific entries. It is crucial to include the DOI (Digital Object Identifier) for the PDB database, which is "10.1093/nar/28.1.235," to ensure proper linking and accessibility.
When citing PDB files in scientific publications, it is also important to consider the specific style guide or formatting requirements of the target journal or publication. Most journals will have their own guidelines for citing databases and online resources, which may include specific instructions for citing the PDB. For instance, the American Chemical Society (ACS) style guide recommends using the following format: "Author(s). (Year). Title of the structure. Protein Data Bank, PDB ID: [PDB entry ID]." Be sure to consult the relevant style guide to ensure compliance with the required citation format.
Furthermore, if you are using PDB data in a software tool, web application, or other digital resource, it is essential to provide proper attribution to the RCSB PDB. This can be achieved by including a clear and visible acknowledgment statement, such as "This product includes data from the RCSB Protein Data Bank (www.rcsb.org), which is supported by funds from the National Science Foundation, the National Institutes of Health, and the US Department of Energy." Additionally, consider including the PDB logo or a hyperlink to the RCSB PDB website to facilitate user access to the original data source.
Lastly, when citing PDB data in educational materials, presentations, or other non-research contexts, it is still crucial to provide proper attribution. Use a simplified citation format that includes the PDB entry ID, author(s), and year of deposition, such as "PDB ID: 1CRN (Berman et al., 2000)." This ensures that users can easily locate the original data source and verifies the credibility of the information presented. By following these PDB format citation guidelines, you can ensure proper acknowledgment of the RCSB Protein Data Bank and its valuable resources, promoting responsible data sharing and scientific collaboration.
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Using DOI for PDB Entries
When citing Protein Data Bank (PDB) entries, using a Digital Object Identifier (DOI) is a standardized and widely accepted method. A DOI provides a persistent link to the specific PDB entry, ensuring that your citation remains accurate and accessible over time. The RCSB Protein Data Bank (PDB) assigns a unique DOI to each structure deposited in the database, making it an ideal choice for academic and scientific citations. To use a DOI for a PDB entry, first locate the specific structure of interest on the RCSB PDB website. Each entry’s page includes a DOI, typically found in the citation section or metadata. This DOI is a crucial piece of information for proper citation.
Once you have identified the DOI, incorporate it into your citation following the format recommended by your citation style guide (e.g., APA, MLA, or Chicago). For example, in APA style, the citation might look like this: "Smith, J., & Doe, A. (Year). Title of the structure. *Protein Data Bank*, *PDB ID*, DOI: [insert DOI here]." Ensure that the DOI is clickable in digital formats to allow readers direct access to the PDB entry. Using the DOI not only enhances the credibility of your citation but also supports the reproducibility of research by providing a direct link to the structural data.
It is important to note that the DOI should always be accompanied by the PDB ID, as the latter is a universally recognized identifier within the structural biology community. The combination of the PDB ID and DOI ensures clarity and avoids confusion, especially when referencing specific structures in discussions or publications. Additionally, including the names of the depositors or authors of the structure, if available, adds context and acknowledges the contributors to the data.
For journals or platforms that require specific citation formats, consult their guidelines to ensure compliance. Many scientific journals prefer or mandate the use of DOIs for data citations, as they align with best practices for data attribution and accessibility. The RCSB PDB also provides pre-formatted citations on each entry’s page, which can be copied and adapted to your citation style, further simplifying the process.
Lastly, using DOIs for PDB entries aligns with broader initiatives to improve data citation practices in scientific research. By adopting this method, researchers contribute to a more transparent and interconnected scientific ecosystem. Always verify the DOI’s accuracy before finalizing your citation, as errors can lead to broken links and hinder access to the referenced data. Properly citing PDB entries with DOIs is a straightforward yet impactful way to uphold academic integrity and facilitate the sharing of structural biology data.
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Citing RCSB PDB in APA Style
When citing the RCSB Protein Data Bank (PDB) in APA style, it is essential to follow the guidelines for referencing online resources. The RCSB PDB is a valuable repository of 3D structure data for proteins, nucleic acids, and other biomolecules, and proper citation ensures that researchers acknowledge the source of structural data used in their work. To begin, the general format for citing an online database like the RCSB PDB in APA style includes the author (or organization), publication year, title, and URL. Since the RCSB PDB is maintained by a consortium, the author field typically includes the RCSB Protein Data Bank as the corporate author.
In APA style, the citation should start with the author, which in this case is the RCSB Protein Data Bank. The publication year for the specific structure or entry should be included, as each PDB entry is updated periodically. For example, if you are citing a specific protein structure, the entry’s release or modification date can be used as the publication year. The title of the citation should include the protein’s name or PDB identifier (e.g., "Hemoglobin, PDB ID: 1GZX"). Following the title, provide the full URL of the specific PDB entry to ensure readers can access the exact resource. For instance, the URL might look like this: https://www.rcsb.org/structure/1GZX.
RCSB Protein Data Bank. (2002). Hemoglobin, PDB ID: 1GZX. https://www.rcsb.org/structure/1GZX
In this example, "2002" is the year the structure was released or last modified, "Hemoglobin" is the protein name, and "PDB ID: 1GZX" is the unique identifier for the structure. The URL directs readers to the specific entry on the RCSB PDB website. If the exact date is unavailable, use the most recent access date or the year the entry was first released.
For general references to the RCSB PDB as a database rather than a specific structure, the citation format changes slightly. In this case, the title should reflect the database itself, and the URL should link to the main RCSB PDB homepage. An example of this citation is:
RCSB Protein Data Bank. (n.d.). RCSB Protein Data Bank. https://www.rcsb.org
Here, "(n.d.)" indicates "no date," as the database is continuously updated and does not have a single publication year. This format is appropriate when acknowledging the RCSB PDB as a resource without referencing a specific structure.
Lastly, consistency and accuracy are key when citing the RCSB PDB in APA style. Ensure that all elements—author, year, title, and URL—are correctly formatted and match the specific structure or resource being cited. Proper citation not only gives credit to the creators and maintainers of the database but also allows readers to locate and verify the structural data used in your research. Always double-check the APA guidelines for any updates, as citation styles may evolve over time.
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MLA Citation for Protein Structures
When citing protein structures from the RCSB Protein Data Bank (PDB) in MLA format, it is essential to provide clear and accurate information to allow readers to locate the specific structure. The MLA citation should include key details such as the PDB ID, title of the structure, authors or contributors, publication year, and the URL of the PDB entry. This ensures proper attribution and facilitates verification of the data.
To begin the citation, start with the PDB ID, which is a unique four-character code assigned to each structure in the database. This should be followed by the full title of the protein structure, enclosed in quotation marks. For example, if citing the structure of hemoglobin, the title might appear as "Structure of Human Hemoglobin." Next, include the names of the authors or contributors who deposited the structure in the PDB. If there are multiple contributors, list them in the order they appear on the PDB entry page.
After the authors, add the publication year of the structure in parentheses. This date can typically be found on the PDB entry page under the "Citation" or "Publication" section. Following the publication year, provide the full URL of the PDB entry, ensuring it is accessible and directs readers to the specific structure. For instance, the URL might look like this:
In addition to the basic citation elements, it is often helpful to include the resolution of the structure (if applicable) and the experimental method used to determine it, such as X-ray crystallography or NMR spectroscopy. This information can be added in parentheses after the publication year or incorporated into the title, depending on the context and relevance to your work. For example, you might write: "Structure of Human Hemoglobin (1.5 Å resolution, X-ray crystallography)."
Finally, ensure consistency and adherence to MLA formatting guidelines throughout the citation. Use a legible font, double-spacing, and proper indentation for any in-text citations or works cited entries. By following these steps, you can create a comprehensive and accurate MLA citation for protein structures from the RCSB PDB, promoting scholarly integrity and facilitating further research in the field of structural biology.
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Acknowledging RCSB PDB in Research
When acknowledging the RCSB Protein Data Bank (PDB) in your research, it is essential to recognize its role as a critical resource for structural biology data. The RCSB PDB provides access to 3D structures of proteins, nucleic acids, and other biomolecules, which are often foundational to scientific studies. Proper acknowledgment ensures compliance with data usage guidelines and gives credit to the infrastructure that supports your research. The RCSB PDB requests that users cite the database in publications, presentations, and other materials that utilize its data or services. This practice not only honors the resource but also helps sustain its funding and development.
To cite the RCSB PDB in your research, include a specific reference to the database in the acknowledgments or methods section of your manuscript. The recommended citation format is: *"Data were obtained from the RCSB Protein Data Bank (www.rcsb.org), with PDB entry codes [list the relevant PDB IDs]."* For example, if you used PDB entries 1ABC and 2XYZ, the citation would read: *"Data were obtained from the RCSB Protein Data Bank (www.rcsb.org), with PDB entry codes 1ABC and 2XYZ."* This ensures clarity and directs readers to the exact data used in your study. Additionally, citing the RCSB PDB’s annual citation paper (e.g., *Acta Crystallographica Section D*) in your reference list is strongly encouraged to acknowledge the ongoing efforts of the resource.
In cases where the RCSB PDB’s tools, software, or web services (e.g., the Molecule of the Month feature, educational materials, or data analysis tools) are utilized, explicitly mention these in your acknowledgments. For instance, you could state: *"We thank the RCSB Protein Data Bank (www.rcsb.org) for providing the [specific tool or resource] used in this study."* This highlights the specific contributions of the RCSB PDB to your research methodology or analysis. If your work involves significant collaboration with RCSB PDB staff or relies heavily on their expertise, consider including a personal acknowledgment to the individuals involved.
For grant applications, reports, or presentations, ensure that the RCSB PDB is acknowledged similarly to how it would be in a publication. Include the full URL (www.rcsb.org) and mention the PDB entry codes or tools used. Visual materials, such as slides or posters, should incorporate the RCSB PDB logo, which can be downloaded from their website, along with a brief acknowledgment statement. This visual recognition reinforces the resource’s role in your work and promotes awareness of its value to the scientific community.
Finally, adhering to the RCSB PDB’s citation guidelines not only fulfills ethical and practical requirements but also contributes to the broader culture of data sharing and attribution in science. By properly acknowledging the RCSB PDB, researchers help maintain the integrity of the resource and ensure its continued availability for future scientific endeavors. For detailed citation guidelines and additional resources, visit the RCSB PDB’s official website, where you can find templates and examples tailored to various research contexts.
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Frequently asked questions
When citing the RCSB PDB, use the following format: "RCSB Protein Data Bank (PDB): [PDB ID] [Year]. Available at [URL]." For example: "RCSB Protein Data Bank (PDB): 1AK4 1996. Available at www.rcsb.org." Additionally, cite the original publication associated with the PDB entry.
Yes, when citing the RCSB PDB website itself, use the following format: "RCSB Protein Data Bank. [Year]. Available at www.rcsb.org. Accessed [Date]." For example: "RCSB Protein Data Bank. 2023. Available at www.rcsb.org. Accessed October 15, 2023."
In the acknowledgments, include a statement such as: "We thank the RCSB Protein Data Bank (www.rcsb.org) for providing access to the structural data used in this study." Ensure you also cite the PDB entry and its original publication in the references.
