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The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

Peter W. Rose, Andreas Prlić, Chunxiao Bi, Wolfgang F. Bluhm, Cole H. Christie, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, John D. Westbrook, Jesse Woo, Jasmine Young, Christine Zardecki (+3 others)
2014 Nucleic Acids Research  
Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education  ...  The RCSB Protein Data Bank (RCSB PDB, http: //www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide.  ...  Peter Troshin contributed the JRonn implementation, used for the protein disorder track of the Protein Feature View. Takanori Nakane developed NDKmol for the RCSB PDB Mobile app.  ... 
doi:10.1093/nar/gku1214 pmid:25428375 pmcid:PMC4383988 fatcat:ms62oq4lnbep5i7dq2qp4f3hwm

Impact Analysis of "Berman HM et al., (2000), The Protein Data Bank"

Jodi Basner
2017 RCSB Protein Data Bank  
In 1998, the Research Collaboratory for Structural Bioinformatics (RCSB) became responsible for the management of the PDB.  ...  Research Data Science & Evaluation Impact of the Protein Data Bank on the Research Community Research Data Science & Evaluation Impact of the Protein Data Bank on the Research Community The PDB has  ...  Research Data Science & Evaluation Impact of the Protein Data Bank on the Research Community What is the Threshold for "Highly Cited"?  ... 
doi:10.2210/rcsb_pdb/pdb-cit-anal-2017 fatcat:odfaoxnry5bglb7eij5vhtcnwy

RCSB Protein Data Bank: sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

Christine Zardecki, Helen M. Berman, Cole Christie, Jose M. Duarte, Zukang Feng, John Westbrook, Jasmine Young, Stephen K. Burley
2018 Acta Crystallographica Section A: Foundations and Advances  
Studies of website usage, bibliometrics, and economics demonstrate the powerful impact of the PDB data on basic and applied research, clinical medicine, education, and the economy.  ...  T he Protein Data Bank (PDB) was established in 1971 as the first open-access digital data resource in biology.  ...  Studies of website usage, bibliometrics, and economics demonstrate the powerful impact of the PDB data on basic and applied research, clinical medicine, education, and the economy.  ... 
doi:10.1107/s0108767318098811 fatcat:wrqm2gm6wzhl3olcu4323oybtu

RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

David S Goodsell, Stephen K Burley
2020 Oncogene  
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  ...  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  ...  Steven Zheng and Shridar Ganesan and other members of the Rutgers Cancer Institute of New Jersey, and contributions from all members of the RCSB PDB and our wwPDB partners around the world.  ... 
doi:10.1038/s41388-020-01461-2 pmid:32939013 pmcid:PMC7581513 fatcat:bhnkikcx6rbxjkqgqzmdzzthmq

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

Stephen K. Burley, Helen M. Berman, Cole Christie, Jose M. Duarte, Zukang Feng, John Westbrook, Jasmine Young, Christine Zardecki
2017 Protein Science  
The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International  ...  RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy.  ...  The PDB is among the most heavily used digital data resources in basic and applied biomedical research and education.  ... 
doi:10.1002/pro.3331 pmid:29067736 pmcid:PMC5734314 fatcat:7jdrdkkw6ffffeu2xpsqp3le4i

PDBe: Protein Data Bank in Europe

Aleksandras Gutmanas, Younes Alhroub, Gary M. Battle, John M. Berrisford, Estelle Bochet, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Swanand P. Gore, Pauline Haslam, Rowan Hatherley (+15 others)
2013 Nucleic Acids Research  
of macromolecular structure data through the single global archive for such data, the PDB.  ...  The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such is actively engaged in the deposition, annotation, remediation and dissemination  ...  They are also particularly indebted to the structural biology community for depositing the fruit of their work in the PDB, BMRB and EMDB archives. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1180 pmid:24288376 pmcid:PMC3965016 fatcat:rv2cpebl5ffzbdppo654oahfly

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Cole H Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M Duarte, Shuchismita Dutta, Zukang Feng (+26 others)
2020 Nucleic Acids Research  
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership  ...  PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.  ...  ACKNOWLEDGEMENTS RCSB PDB is a member of the Worldwide Protein Data Bank (wwPDB.org).  ... 
doi:10.1093/nar/gkaa1038 pmid:33211854 pmcid:PMC7779003 fatcat:dkqo54quqjgovp7y4v67b635zu

The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology

David S. Goodsell, Shuchismita Dutta, Christine Zardecki, Maria Voigt, Helen M. Berman, Stephen K. Burley
2015 PLoS Biology  
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.  ...  Jesse Woo, for their support in organizing and presenting this project.  ... 
doi:10.1371/journal.pbio.1002140 pmid:25942442 pmcid:PMC4420264 fatcat:mq3g6lso4jcpvlvc6empbdfkwi

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

A. R. Kinjo, H. Suzuki, R. Yamashita, Y. Ikegawa, T. Kudou, R. Igarashi, Y. Kengaku, H. Cho, D. M. Standley, A. Nakagawa, H. Nakamura
2011 Nucleic Acids Research  
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized  ...  FUNDING Funding for open access charge: National Bioscience Database Center, the Japan Science and Technology Agency. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr811 pmid:21976737 pmcid:PMC3245181 fatcat:rgdsfxvkfvhgnnpag3funh52pu

Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences

Shuchismita Dutta, Christine Zardecki, David S. Goodsell, Helen M. Berman
2010 Journal of Applied Crystallography  
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  ...  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  ...  It is funded by the NSF, NIGMS, DOE, NLM, NCI, NINDS and NIDDK (grant No. DBI0829586). We thank all the RCSB PDB staff for their enthusiasm and participation in education and outreach activities.  ... 
doi:10.1107/s002188981002371x pmid:20877496 pmcid:PMC2943739 fatcat:tumibltfefcxzomabkgef2vkmq

Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development

Stephen K. Burley
2021 Journal of Biological Chemistry  
Finally, the author gratefully acknowledges contributions to the success of the PDB archive made by all members of RCSB PDB (past and present) and our Worldwide Protein Data Bank partners (Protein Data  ...  Bank in Europe, Protein Data Bank Japan, Biological Magnetic Resonance Bank, and Electron Microscopy Data Bank).  ...  Availability of the Protein Data Bank archive helps transform 3D structure data to knowledge, benefiting basic and applied research and education.  ... 
doi:10.1016/j.jbc.2021.100559 pmid:33744282 fatcat:7aumkkjssrbn3mmx5k4jwvenoa

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.  ...  Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands.  ...  Acknowledgements The authors thank all the members of the worldwide Protein Data Bank (wwPDB) for their support and feedback, Kim Henrick for his direction to the PDB in Europe (PDBe) biocuration team  ... 
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata (+4 others)
2017 Protein Science  
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures.  ...  surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.  ...  years, by adding newly determined structures every week. 11 The database has been widely used for various types of research, and is also useful for education, by providing concrete views of biomolecules  ... 
doi:10.1002/pro.3273 pmid:28815765 pmcid:PMC5734392 fatcat:7ttn55ucxvcjfjkmivznvmet34

Crystallography and Databases

Ian Bruno, Saulius Gražulis, John R Helliwell, Soorya N Kabekkodu, Brian McMahon, John Westbrook
2017 Data Science Journal  
A session at SciDataCon2016 gave an overview of the largest extant crystallographic databases and their current activities and plans for the future.  ...  Crystallographic databases have existed as electronic resources for over 50 years, and have provided comprehensive archives of crystal structures of inorganic, organic, metal-organic and biological macromolecular  ...  The RCSB PDB is supported by the National Science Foundation (DBI 1338415), National Institutes of Health, and the Department of Energy; PDBe by the Wellcome Trust, BBSRC, MRC, EU, CCP4, and EMBL-EBI;  ... 
doi:10.5334/dsj-2017-038 fatcat:d7adzhjqxvf4zfcfzgaen2qf3e

Molecular Illustration in Research and Education: Past, Present, and Future

David S. Goodsell, Jodie Jenkinson
2018 Journal of Molecular Biology  
Building on decades of experience in design, best practices resources are available to guide creation of illustrations that are effective for research and education communities.  ...  2D illustration is used extensively to study and disseminate the results of structural molecular biology.  ...  US Department of Energy (DSG) and SIG 13/14 from the Social Sciences and Humanities Research Council (SSHRC) (JJ).  ... 
doi:10.1016/j.jmb.2018.04.043 pmid:29752966 pmcid:PMC6186494 fatcat:r4zme3rq7rfz7cnfe6nayyl2aq
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