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RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study
David S Goodsell1,2, Stephen K Burley3,4,5,6
1Research Collaboratory for Structural Bioinformatics Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA. David.Goodsell@rcsb.org.
Abstract:
Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public. We exemplify the value of understanding cancer-related proteins in 3D with a case study focused on human papillomavirus.
Insights
Atomic-level 3D structures of cancer proteins are crucial for understanding cancer mechanisms and developing new drugs. The RCSB PDB offers free access to this vital data, aiding researchers and patients globally.
Area of Science:
- Structural Biology
- Biochemistry
- Oncology
Background:
- Atomic-level 3D structure data of biological macromolecules are essential for understanding cancer-related protein functions in oncogenesis, proliferation, and metastasis.
- These structures are critical for identifying drug targets and developing novel therapeutics for cancer treatment.
- The Protein Data Bank (PDB) is an open-access repository for 3D biomolecular structures, widely utilized in drug discovery and biomedical research.
Purpose of the Study:
- To review the online resources provided by the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB).
- To highlight the accessibility and utility of these resources for diverse user groups, including researchers, educators, and patients.
- To demonstrate the importance of 3D protein structures in cancer research through a case study.
Main Methods:
- Review of publicly available online resources from the RCSB PDB.
- Analysis of the PDB archive for data relevant to cancer research.
- Case study focusing on human papillomavirus (HPV) to illustrate the application of 3D structural data.
Main Results:
- The RCSB PDB provides a streamlined portal to the PDB archive, offering free access to millions of 3D biomolecular structures.
- These resources support a wide range of users, from basic researchers to patients, in areas like drug discovery and education.
- The case study on HPV exemplifies how 3D structural information aids in understanding viral proteins and their role in cancer.
Conclusions:
- RCSB PDB resources are invaluable for advancing cancer research and drug development by providing free access to critical 3D structural data.
- Understanding the 3D structures of cancer-related proteins is fundamental for mechanistic insights and therapeutic strategies.
- The accessibility of PDB data empowers a broad community, fostering innovation in cancer treatment and education.
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