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The RCSB PDB information portal for structural genomics

A. Kouranov
2006 Nucleic Acids Research  
10 The RCSB Protein Data Bank (PDB) offers online tools, summary reports and target information related to the worldwide structural genomics initiatives from its portal at  ...  assessment of the progress of structural genomics based on the functional coverage of the human genome by PDB structures, structural genomics targets and homo-25 logy models.  ...  The RCSB PDB is a member of the wwPDB.  ... 
doi:10.1093/nar/gkj120 pmid:16381872 pmcid:PMC1347482 fatcat:52gyctuk2jcybonlpaq3qp4gcu

RCSB Protein Data Bank 1D3D module: Displaying positional features on macromolecular assemblies

Joan Segura, Yana Rose, Sebastian Bittrich, Stephen K Burley, Jose M Duarte, Lenore Cowen
2022 Bioinformatics  
Availability Supplementary information Supplementary data are available at Bioinformatics online.  ...  annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level.  ...  Currently, the RCSB PDB web portal uses this tool to display an interacting mapping between 1D protein features and the 3D structures of biomolecules. .  ... 
doi:10.1093/bioinformatics/btac317 pmid:35543462 fatcat:4w75lokparcrlo4jxezno3dzqa

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.'  ...  Zhuravleva and the entire RCSB PDB team.  ... 
doi:10.1093/nar/gkw1000 pmid:27794042 pmcid:PMC5210513 fatcat:7snb5xj2bjbxxklorxm5kwax6i

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh (+28 others)
2018 Nucleic Acids Research  
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB,, the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania  ...  Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals  ...  ACKNOWLEDGEMENTS RCSB PDB is a member of the Worldwide Protein Data Bank (  ... 
doi:10.1093/nar/gky1004 pmid:30357411 pmcid:PMC6324064 fatcat:clctmqo6ujaifm7s27vk3s2h7i

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  ...  RCSB PDB is jointly funded by grants to SKB from the National Science Foundation (DBI-1832184), the US Department of  ... 
doi:10.1038/s41388-020-01461-2 pmid:32939013 pmcid:PMC7581513 fatcat:bhnkikcx6rbxjkqgqzmdzzthmq

The protein structure initiative structural genomics knowledgebase

H. M. Berman, J. D. Westbrook, M. J. Gabanyi, W. Tao, R. Shah, A. Kouranov, T. Schwede, K. Arnold, F. Kiefer, L. Bordoli, J. Kopp, M. Podvinec (+5 others)
2009 Nucleic Acids Research  
This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available  ...  The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structural has been created to turn the products of the PSI structural genomics effort into knowledge  ...  Cross-references are provided to the Research Collaboratory for Structural Biology (RCSB) PDB (5), Pfam (6), Superfamily (7), TIGR Families (8), ProDom (9), iProClass (10) and Prosite (11) .  ... 
doi:10.1093/nar/gkn790 pmid:19010965 pmcid:PMC2686438 fatcat:edk423qxwrdkfhuakisra3dfkm

Integration of macromolecular complex data into the Saccharomyces Genome Database

2019 Database: The Journal of Biological Databases and Curation  
In addition, detailed information about how subunits interact within the complex, their stoichiometry and the physical structure are displayed when such information is available.  ...  Information on macromolecular complexes will continue to be updated in collaboration with the Complex Portal team and curated as more data become available.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health.  ... 
doi:10.1093/database/baz008 pmid:30715277 pmcid:PMC6360207 fatcat:qfslz3voprekllrvrfd2lkhdlq

Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank

Wendy A. Warr
2008 Journal of Computer-Aided Molecular Design  
Goodsell about PSI structures similar to his Molecule of the Month column at the RCSB PDB.  ...  HMB: The RCSB PDB is funded by grants from the United States funding agencies, but the funding mechanisms for PDB worldwide are not what they should be for this kind of resource.  ... 
doi:10.1007/s10822-008-9234-3 pmid:18781281 fatcat:eqydoyxfk5dgjolojj45huaszy

Protein Structure Annotation Resources [chapter]

Margaret J. Gabanyi, Helen M. Berman
2014 Msphere  
Since the 3-D structure of proteins are ultimately responsible for most actions in the cell, this review will focus on protein structure annotation resources that aim to explain a  ...  Therefore, to maximize the amount of information garnered from the genes, proteins, and structures we do study, annotations are captured in the hopes that they may apply to similar (homologous) proteins  ...  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

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 RCSB PDB serves as the global Archive Keeper for the wwPDB.  ...  During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and  ...  The RCSB PDB website ( systematizes and integrates structural information with 40 external data resources for our Data Consumers.  ... 
doi:10.1002/pro.3331 pmid:29067736 pmcid:PMC5734314 fatcat:7jdrdkkw6ffffeu2xpsqp3le4i

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.  ...  We thank our users and our current and past website developers, particularly Boki Beran, Chunxiao Bi, Wolfgang Bluhm, Cole Christie, Andreas Prlić, Greg Quinn, Alex Ramos, Peter Rose, and Jesse Woo, for  ... 
doi:10.1371/journal.pbio.1002140 pmid:25942442 pmcid:PMC4420264 fatcat:mq3g6lso4jcpvlvc6empbdfkwi

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 ( 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 (  ... 
doi:10.1093/nar/gkaa1038 pmid:33211854 pmcid:PMC7779003 fatcat:dkqo54quqjgovp7y4v67b635zu

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  ...  The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as  ...  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

Integrative illustration for coronavirus outreach

David S. Goodsell, Maria Voigt, Christine Zardecki, Stephen K. Burley
2020 PLoS Biology  
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.  ...  Acknowledgments This is manuscript 29976 from the Scripps Research Institute.  ... 
doi:10.1371/journal.pbio.3000815 pmid:32760062 pmcid:PMC7433897 fatcat:ealkhq3mcvhczjmcrg4dc4xcru

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

Margaret J. Gabanyi, Paul D. Adams, Konstantin Arnold, Lorenza Bordoli, Lester G. Carter, Judith Flippen-Andersen, Lida Gifford, Juergen Haas, Andrei Kouranov, William A. McLaughlin, David I. Micallef, Wladek Minor (+6 others)
2011 Journal of Structural and Functional Genomics  
For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models  ...  The Protein Structure Initiative's Structural Biology Knowledgebase (SBKB, URL: is an open web resource designed to turn the products of the structural genomics and structural biology  ...  Acknowledgments The SBKB is a resource center within the Protein Structure Initiative and is supported by grant U01 GM093324-01 from the National Institute of General Medical Sciences.  ... 
doi:10.1007/s10969-011-9106-2 pmid:21472436 pmcid:PMC3123456 fatcat:335qzn5h3relxbq4n7lomjdcpa
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