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Integrative illustration for coronavirus outreach
2020
PLoS Biology
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Two illustrations integrate current knowledge about severe acute respiratory syndrome (SARS) coronaviruses and their life cycle. They have been widely used in education and outreach through free distribution as part of a coronavirus-related resource at Protein Data Bank (PDB)-101, the education portal of the RCSB PDB. Scientific sources for creation of the illustrations and examples of dissemination and response are presented.
doi:10.1371/journal.pbio.3000815
pmid:32760062
pmcid:PMC7433897
fatcat:ealkhq3mcvhczjmcrg4dc4xcru
John D. Westbrook Jr (1957–2021)
2021
Acta Crystallographica Section D: Structural Biology
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He was incredibly beloved and respected by his colleagues at Rutgers and worldwide, known for his dry wit and endless enthusiasm for thinking about all aspects of data and data management. John had a long and highly successful career developing ontologies, tools, and infrastructure in data acquisition, validation, standardization, and mining in the structural biology and life science domains. His work established the PDBx/mmCIF data dictionary and format as the foundation of the modern Protein
doi:10.1107/s2059798321011402
pmid:34726174
pmcid:PMC8561733
fatcat:jzjo3dw5cvayrmxi32vnljm5be
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... ata Bank (PDB) archive (wwPDB.org). More than twenty-five years ago, while still a graduate student, John recognized the importance of a well defined data model to ensure high-quality and reliable structural information to data users. He was the principal architect of the mmCIF data representation for biological macromolecular data. Data are presented in either key-value or tabular form based on a simple, context-free grammar (without column width constraints). All relationships between common data items (e.g. atom and residue identifiers) are explicitly documented within the PDBx Exchange Dictionary (https:// mmcif.wwpdb.org). The use of the PDBx/mmCIF format enables software applications to evaluate and validate referential integrity within any PDB entry. A key strength of the
Interesting Structures: Education and Outreach at the RCSB Protein Data Bank
2008
PLoS Biology
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Analysis of impact metrics for the Protein Data Bank
2018
Scientific Data
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Since 1971, the Protein Data Bank (PDB) archive has served as the single, global repository for open access to atomic-level data for biological macromolecules. The archive currently holds >140,000 structures (>1 billion atoms). These structures are the molecules of life found in all organisms. Knowing the 3D structure of a biological macromolecule is essential for understanding the molecule's function, providing insights in health and disease, food and energy production, and other topics of
doi:10.1038/sdata.2018.212
pmid:30325351
pmcid:PMC6190746
fatcat:6o4xdmnaenadzbbsvgzekefwye
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... ern to prosperity and sustainability. PDB data are freely and publicly available, without restrictions on usage. Through bibliometric and usage studies, we sought to determine the impact of the PDB across disciplines and demographics. Our analysis shows that even though research areas such as molecular biology and biochemistry account for the most usage, other fields are increasingly using PDB resources. PDB usage is seen across 150 disciplines in applied sciences, humanities, and social sciences. Data are also re-used and integrated with >400 resources. Our study identifies trends in PDB usage and documents its utility across research disciplines.
The Nucleic Acid Database: A Resource for Nucleic Acid Science
1998
Acta Crystallographica Section D: Biological Crystallography
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The Nucleic Acid Database (NDB) distributes information about nucleic acid-containing structures. Here the information content of the database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular databases is given.
doi:10.1107/s0907444998007926
pmid:10089485
fatcat:nbyyiyzajraffc2xjcfsu73hpm
Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive
2017
Structure
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Zardecki RCSB PDB; Rutgers, The State University of New Jersey Stephen K. ...
Huanwang Yang RCSB PDB; Rutgers, The State University of New Jersey John D Westbrook RCSB PDB; Rutgers, The State University of New Jersey Jasmine Young RCSB PDB; Rutgers, The State University of New Jersey Christine ...
doi:10.1016/j.str.2017.01.013
pmid:28216043
pmcid:PMC7182075
fatcat:kojf7bk2ijcvlfkkeg5m2vp56m
Impact of the Protein Data Bank Across Scientific Disciplines
2020
Data Science Journal
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Christine Zardecki and Stephen K. Burley designed the study and finalized and approved the manuscript. ...
doi:10.5334/dsj-2020-025
fatcat:2ahclmqdmbaddmvhr6sj4nonma
Molecular storytelling for structural biology outreach and education
2020
Acta Crystallographica Section A: Foundations and Advances
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Knowledge about the structure and function of biomolecules continues to grow exponentially, enabling us to "see" structural snapshots of biomolecular interactions and functional assemblies. At PDB-101, the educational portal of the RCSB Protein Data Bank, we have taken a storytelling approach to make this body of knowledge accessible and comprehensible to a wide community of students, educators and the general public. For 20 years, the Molecule of the Month series has utilized a traditional
doi:10.1107/s0108767320099900
fatcat:ueybdthjd5fetd4yjfdn4ow5xe
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... strated storytelling approach that is regularly adapted for classroom instruction. Similar visual and interactive storytelling approaches are used to present topical subjects at PDB-101, and full curricular materials for building a detailed narrative around topics of particular interest. This emphasis on storytelling led to the Video Challenge for High School students, now in its 7th year. In this workshop, I will present some of the lessons we have learned for teaching and communicating structural biology using the PDB archive of biomolecular structures. PDB-101 and the RCSB PDB are funded by the National Science Foundation
The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology
2015
PLoS Biology
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The Research Collaboratory for Structural Bioinformatics (RCSB) Molecule of the Month series provides a curated introduction to the 3-D biomolecular structures available in the Protein Data Bank archive and the tools that are available at the RCSB website for accessing and exploring them. A variety of educational materials, such as articles, videos, posters, hands-on activities, lesson plans, and curricula, build on this series for use in a variety of educational settings as a general
doi:10.1371/journal.pbio.1002140
pmid:25942442
pmcid:PMC4420264
fatcat:mq3g6lso4jcpvlvc6empbdfkwi
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... on to key topics, such as enzyme action, protein synthesis, and viruses. The series and associated educational materials are freely available at www.rcsb.org.
Delving into COVID-19 'seams': examining the structural fabric of SARS-CoV-2
2020
Acta Crystallographica Section A: Foundations and Advances
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The year 2019 and 2020 took an unprecedented turn as SARS-CoV-2 (COVID-19) ravaged the world, taking over half a million lives (as of July 2020), leaving vulnerable communities to take the hardest hits, exacerbating systemic injustices towards minorities (including decreased access to healthcare), and damaging economies. By examining proteins and their respective mutations in SARS-CoV-2, a better understanding of its structural biology can aid in drug and vaccine discovery. Further applications
doi:10.1107/s0108767320097767
fatcat:sdcwwmwwlrb75a2zhcvfqupay4
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... of a deepened structural understanding of SARS-CoV-2 include assisting in broader research efforts and valuable public health efforts to mitigate and prevent harm caused by SARS-CoV-2 and other coronaviruses worldwide. As part of a virtual summer research experience with the RCSB PDB, we studied how SARS-CoV-2 proteins protein evolved during the first six months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure using various structural bioinformatics tools, including Clustal Omega (www.ebi.ac.uk/Tools/msa/clustalo/) for sequence alignments and phylogenetic trees; Mol* (molstar.org) for 3D molecular visualization; and Foldit (fold.it) for structural/energetic effects of sequence mutations. The focus of this poster is SARS-CoV-2 Orf7a, a viral protein that interferes with N-linked glycosylation of the cellular protein BST-2, an inhibitor of coronavirus release (Taylor et al. 2015). Orf7a has also been shown to arrest cells in the G0/G1 cell checkpoint during SARS-CoV infection, thereby preventing cell cycle progression. The G0/G1 cell checkpoint is a phase in the cell division process wherein DNA is checked for damage before allowing progress into the S phase. If DNA damage cannot be repaired cell death ensues. Prevention of cell cycle progression is thought to provide more time for coronaviruses to replicate at higher rates with increased nucleotide pools and allow for higher virus pathogenicity (Yuan et al. 2005). Studying Orf7a can provide insights into SARS-CoV-2 pathogenesis, including what proteins are involved in regulating viral propagation and what SARS-CoV-2 proteins affect host cell cycle regulation.
Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences
2010
Journal of Applied Crystallography
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The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that
doi:10.1107/s002188981002371x
pmid:20877496
pmcid:PMC2943739
fatcat:tumibltfefcxzomabkgef2vkmq
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... sent macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health.
Structural analysis of severe acute respiratory syndrome coronavirus-2 proteins: exploring mutations in Nsp13
2020
Acta Crystallographica Section A: Foundations and Advances
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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), discovered in December 2019, caused the COVID-19 global pandemic. SARS-CoV-2 belongs to the family, Coronaviridae, which is composed of positivestranded RNA viruses. These viruses are known to have one of the largest RNA viral genomes, which consists of approximately thirty-thousand base pairs. The SARS-CoV-2 genome encodes both non-structural proteins, which assist in replication of the virus upon infection, and various structural
doi:10.1107/s0108767320097779
fatcat:v2umejxjuzhftmmlk56mbf55ki
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... d assembly proteins. As part of a virtual summer research experience with the RCSB PDB, we studied how SARS-CoV-2 proteins protein evolved during the first six months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure using various structural bioinformatics tools, including Clustal Omega (www.ebi.ac.uk/Tools/msa/clustalo/) for sequence alignments and phylogenetic trees; Mol* (molstar.org) for 3D molecular visualization; and Foldit (fold.it) for structural/energetic effects of sequence mutations. The focus of this poster is SARS-CoV-2 non-structural protein 13 (Nsp13), a 596-residue protein consisting of five domains. Nsp13 functions as a helicase, unwinding double-stranded RNA. Helicase activity depends on NTP hydrolysis, catalyzed by six conserved active site residues. Nsp13 synergizes with the viral RNA-dependent RNA polymerase, a heterotetramer consisting of once copy of Nsp7, two copies of Nsp8, and one copy of Nsp12. Nsp13 represents a potential target for discovery and development for small molecules that combat SARS-CoV-2. Studying the structure of this protein will enhance our understanding of its mechanism of action and ways to inhibit the enzyme. Figure 1.
Transactions from the 70th Annual Meeting of the American Crystallographic Association: Structural Science—New Ways to Teach the Next Generation
2021
Structural Dynamics
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Multivariate analyses of quality metrics for crystal structures in the PDB archive
2017
Acta Crystallographica Section A: Foundations and Advances
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Zardecki RCSB PDB; Rutgers, The State University of New Jersey Stephen K. ...
Huanwang Yang RCSB PDB; Rutgers, The State University of New Jersey John D Westbrook RCSB PDB; Rutgers, The State University of New Jersey Jasmine Young RCSB PDB; Rutgers, The State University of New Jersey Christine ...
doi:10.1107/s0108767317098142
fatcat:lhfv6ht5pbbuhmitc2djjzd63q
Trendspotting in the Protein Data Bank
2013
FEBS Letters
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The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85 000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data.
doi:10.1016/j.febslet.2012.12.029
pmid:23337870
pmcid:PMC4068610
fatcat:pc6muagsrzh6lcqjm4ewkct5sa
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