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The RCSB Protein Data Bank: redesigned web site and web services

P. W. Rose, B. Beran, C. Bi, W. F. Bluhm, D. Dimitropoulos, D. S. Goodsell, A. Prlic, M. Quesada, G. B. Quinn, J. D. Westbrook, J. Young, B. Yukich (+3 others)
2010 Nucleic Acids Research  
The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base.  ...  data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources.  ...  We thank Sean Van Tyne and the San Diego User Experience Special Interest Group (http://www.uxsig.org) for an in-depth usability review of the RCSB web site that led to many improvements.  ... 
doi:10.1093/nar/gkq1021 pmid:21036868 pmcid:PMC3013649 fatcat:aciwaivaenfubmhs2r3tc37qiu

The distribution and query systems of the RCSB Protein Data Bank

P. E. Bourne
2004 Nucleic Acids Research  
The Protein Data Bank (PDB; http://www.pdb.org) is the primary source of information on the 3D structure of biological macromolecules.  ...  The current query and distribution system is described and an alpha version of the future re-engineered system introduced.  ...  in Biotechnology (CARB) at the National Institute of Standards and Technology (NIST)Ðthree members of the Research Collaboratory for Structural Bioinformatics (RCSB).  ... 
doi:10.1093/nar/gkh096 pmid:14681399 pmcid:PMC308830 fatcat:o6qlkzgql5h6nf34lx4b67dbea

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

N. Deshpande
2004 Nucleic Acids Research  
The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules.  ...  The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data.  ...  ACKNOWLEDGEMENTS The RCSB PDB is operated by Rutgers, The State University of New Jersey; the San Diego Supercomputer Center (SDSC) at the University of California San Diego (UCSD); and the Center for  ... 
doi:10.1093/nar/gki057 pmid:15608185 pmcid:PMC540011 fatcat:r5c6q6654fbzvb6kkuk356k4du

PDBe: Protein Data Bank in Europe

S. Velankar, Y. Alhroub, A. Alili, C. Best, H. C. Boutselakis, S. Caboche, M. J. Conroy, J. M. Dana, G. van Ginkel, A. Golovin, S. P. Gore, A. Gutmanas (+21 others)
2010 Nucleic Acids Research  
Finally, the entire web site has been redesigned to make it substantially easier to use for expert and novice users alike.  ...  The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank  ...  depositing their structures and experimental data in the PDB and EMDB.  ... 
doi:10.1093/nar/gkq985 pmid:21045060 pmcid:PMC3013808 fatcat:732ckrjoq5afnk3jt2i7jwjcvy

The Protein Data Bank

Helen M. Berman, Tammy Battistuz, T. N. Bhat, Wolfgang F. Bluhm, Philip E. Bourne, Kyle Burkhardt, Zukang Feng, Gary L. Gilliland, Lisa Iype, Shri Jain, Phoebe Fagan, Jessica Marvin (+7 others)
2002 Acta Crystallographica Section D: Biological Crystallography  
The Protein Data Bank [PDB; Berman, Westbrooket al.(2000),Nucleic Acids Res.28, 235–242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules.  ...  This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource.  ...  The Protein Data Bank does not recommend or endorse any speci®c commercial software products.  ... 
doi:10.1107/s0907444902003451 pmid:12037327 fatcat:satbdpl4a5c2jk7uo42ovv2dgm

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
2016 Nucleic Acids Research  
The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (ww-PDB), accepts and processes the deposited data of experimentally determined macromolecular structures  ...  We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former.  ...  T. thanks Shigeru Endo for helping with the ProMode Elastic service.  ... 
doi:10.1093/nar/gkw962 pmid:27789697 pmcid:PMC5210648 fatcat:pan6qdrpe5bknfgkot6blgnp6u

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  
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  ...  of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.  ...  ACKNOWLEDGEMENTS The authors would like to thank all collaborators and partners in the EBI, EMBL, wwPDB, EMDataBank, BioMagResBank, CCPN, CCP4, CCDC and other collaborative efforts.  ... 
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  ...  During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB  ...  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

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

Robert D. Finn, Benjamin L. Miller, Jody Clements, Alex Bateman
2013 Nucleic Acids Research  
The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular  ...  This allows for independent development, improving data access and giving clearer separation between the protein family and interactions datasets.  ...  ACKNOWLEDGEMENTS We would like to thank Travis Wheeler for help in preparing the manuscript and Goran Ceric and his team for Janelia Farm's high performance computing resources.  ... 
doi:10.1093/nar/gkt1210 pmid:24297255 pmcid:PMC3965099 fatcat:be5pgdwc3rgdrdqvuopxc5uwum

OUP accepted manuscript

2016 Nucleic Acids Research  
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb. org), the US data center for the global PDB archive, makes PDB data freely available to all users, from  ...  New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.'  ...  ACKNOWLEDGEMENTS RCSB PDB is a member of the Worldwide Protein Data Bank (wwPDB.org).  ... 
doi:10.1093/nar/gkw1000 pmid:27794042 pmcid:PMC5210513 fatcat:7snb5xj2bjbxxklorxm5kwax6i

Protein Structure Annotation Resources [chapter]

Margaret J. Gabanyi, Helen M. Berman
2014 Msphere  
Protein Data Bank archive (v. 2014-03-25) (3, 4).  ...  The different levels of annotation data (primary vs. derived vs. inferred) will also be described and how they should all be considered accordingly.  ...  Acknowledgments The authors are grateful to B. Coimbatore Narayanan, G. Gabanyi  ... 
doi:10.1007/978-1-4939-2230-7_1 pmid:25502191 pmcid:PMC5586544 fatcat:n4wrlx7rtvfy7mya7w457ppwca

Digital archives for molecular microscopy

Christoph Best, Matthew Dougherty
2010 Proceedings of the 1st International Digital Preservation Interoperability Framework Symposium on - INTL-DPIF '10  
The Electron Microscopy Data Bank (EMDB) [1] is the global repository for the Internet retrieval of high-resolution threedimensional images of macromolecular complexes and subcellular structures.  ...  Established in 2002 at the European Bioinformatics Institute (EBI), it is now an international effort of EBI, Rutgers University (RCSB) in New Jersey, and the National Center for Macromolecular Imaging  ...  ACKNOWLEDGMENTS EMDB is supported by grants from the U.S. National Institutes of Health (grant nr. R01GM079429) and from the UK Biotechnology and Biological Sciences Research Council (grant nr.  ... 
doi:10.1145/2039263.2039267 fatcat:2soluujaljbj3pz7mjs2olyzne

A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules

R. Huhne, F.-T. Koch, J. Suhnel
2007 Briefings in Functional Genomics & Proteomics  
As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for  ...  Both the primary and secondary resources often merge the information in the PDB files with data from other resources and offer additional analysis tools thereby adding value to the original PDB data.  ...  The authors are grateful to Kristina Mehliss who has helped with thumbnail image generation, to Friedrich Haubensak for maintaining the web server and to Stefan Westermeier for working on the QuickSearch  ... 
doi:10.1093/bfgp/elm020 pmid:17956938 fatcat:6mtu2bifpbarhorqxhkgq7xwna

The PSIPRED Protein Analysis Workbench: 20 years on

2019 Nucleic Acids Research  
We additionally discuss any new software, the new hardware infrastructure, our webservices and web site.  ...  Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years.  ...  ACKNOWLEDGMENTS The following people have contributed server code, methods or updates to the PSIPRED web server and workbench over the previous 20 years: Michael Sadowski, Sean Ward, Domenico Cozzetto,  ... 
doi:10.1093/nar/gkz297 pmid:31251384 pmcid:PMC6602445 fatcat:b7bxg2ft4fhbdeyro3fpwgriue

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.  ...  This review summarizes these presentations and considers them alongside other players in the field, demonstrating their variety, versatility and focus on quality and usefulness.  ...  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
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