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Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank

Andreas Prlić, Tara Kalro, Roshni Bhattacharya, Cole Christie, Stephen K. Burley, Peter W. Rose
2016 Bioinformatics  
This integration bridges from the human genome across protein sequence to 3D structure space.  ...  The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules.  ...  to 3D atomic level structural information.  ... 
doi:10.1093/bioinformatics/btw547 pmid:27551105 pmcid:PMC5167066 fatcat:l4rrzkjyafgyhlx45uzgrexd5y

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  
annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level.  ...  Availability https://github.com/rcsb/rcsb-saguaro-3d. Supplementary information Supplementary data are available at Bioinformatics online.  ...  annotations from multiple resources and visualizes them at 1D sequence and 3D structure levels.  ... 
doi:10.1093/bioinformatics/btac317 pmid:35543462 fatcat:4w75lokparcrlo4jxezno3dzqa

OUP accepted manuscript

2016 Nucleic Acids Research  
PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways.  ...  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  ...  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

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  
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.  ...  Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.  ...  Robert Hanson helped with Jmol/JSmol and the crystal packing and binding site display during his mini-sabbatical at the RCSB PDB at UCSD.  ... 
doi:10.1093/nar/gku1214 pmid:25428375 pmcid:PMC4383988 fatcat:ms62oq4lnbep5i7dq2qp4f3hwm

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, rcsb.org), 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  ...  We gratefully acknowledge contributions from past members of the RCSB PDB team and our Worldwide Protein Data Bank partners.  ... 
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  
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  ...  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  ...  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 PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy.  ...  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 (RCSB.org) 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

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  ...  , serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around  ...  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

Protein Structure Annotation Resources [chapter]

Margaret J. Gabanyi, Helen M. Berman
2014 Msphere  
in the Protein Data Bank archive (v. 2014-03-25) (3, 4).  ...  A key reason three-dimensional (3-D) protein structures are annotated with supporting or derived information is to understand the molecular basis of protein function.  ...  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

Unified Data Resource for Cryo-EM [chapter]

Catherine L. Lawson
2010 Methods in Enzymology  
The resource unifies public access to the two major EM Structural Data archives: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular  ...  EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB), and the National Center for Macromolecular Imaging (NCMI), is  ...  world-wide PDB (wwPDB, Berman et al., 2003) , a consortium consisting of the RCSB PDB (www.pdb.org), the Protein Data Bank in Europe (PDBe) at EBI (www.ebi.ac.uk/pdbe), the Protein Data Bank Japan (PDBj  ... 
doi:10.1016/s0076-6879(10)83004-6 pmid:20888470 pmcid:PMC2966391 fatcat:ncsypzwkdvh6dopessk56ubpaq

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

Impact of genetic variation on three dimensional structure and function of proteins

Roshni Bhattacharya, Peter W. Rose, Stephen K. Burley, Andreas Prlić, Yang Zhang
2017 PLoS ONE  
The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings.  ...  at the DNA level.  ...  Acknowledgments We thank Hagen Tilgner, Lilia Iakoucheva, and Roser Corominas for useful discussions, Sajani Swamy for feedback on the manuscript.  ... 
doi:10.1371/journal.pone.0171355 pmid:28296894 pmcid:PMC5351996 fatcat:fu6vzdo4hjdrliuimow2h56xe4

EMDataBank.org: unified data resource for CryoEM

C. L. Lawson, M. L. Baker, C. Best, C. Bi, M. Dougherty, P. Feng, G. van Ginkel, B. Devkota, I. Lagerstedt, S. J. Ludtke, R. H. Newman, T. J. Oldfield (+10 others)
2010 Nucleic Acids Research  
The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules  ...  EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a  ...  ACKNOWLEDGEMENTS We are grateful to Tom Goddard for integrating the EMDataBank.org web service into UCSF Chimera. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq880 pmid:20935055 pmcid:PMC3013769 fatcat:ipujineisngezfbkud2ltei7eq

BioMagResBank

E. L. Ulrich, H. Akutsu, J. F. Doreleijers, Y. Harano, Y. E. Ioannidis, J. Lin, M. Livny, S. Mading, D. Maziuk, Z. Miller, E. Nakatani, C. F. Schulte (+4 others)
2007 Nucleic Acids Research  
BMRB is a partner in the Worldwide Protein Data Bank (wwPDB).  ...  author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules  ...  Data Bank Japan (PDBj), the National Magnetic Resonance Facility at Madison (NMRFAM), the Collaborative Computational Program on NMR (CCPN), the European Bioinformatics Institute (EBI) and the Condor  ... 
doi:10.1093/nar/gkm957 pmid:17984079 pmcid:PMC2238925 fatcat:t5ldblf4cjbs7ojw5y4xriuoym

PROTEIN INFORMATICS TOWARDS INTEGRATION OF DATA GRID AND COMPUTING GRID

HARUKI NAKAMURA
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
Information of the structures and functions of protein molecules and their mutual interactions that construct protein networks increases rapidly as the consequence of the structural genomics and structural  ...  data from the varieties of heterogeneous biological databases [2] .  ...  Our laboratory develops an advanced database for Protein Data Bank Japan (PDBj), collaborating with Research Collaboratory for Structural Bioinformatics (RCSB) in USA, and Macromolecular Structure Database  ... 
doi:10.1142/9781860947322_0036 fatcat:gptx3memwfgwdihk6uv3ujvaoy
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