- The RCSB protein data bank: integrative view of protein, gene and 3D structural information. [PMID: 27794042]
Peter W Rose, Andreas Prlić, Ali Altunkaya, Chunxiao Bi, Anthony R Bradley, Cole H Christie, Luigi Di Costanzo, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Rachel Kramer Green, David S Goodsell, Brian Hudson, Tara Kalro, Robert Lowe, Ezra Peisach, Christopher Randle, Alexander S Rose, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D Westbrook, Jesse Woo, Huangwang Yang, Jasmine Y Young, Christine Zardecki, Helen M Berman, Stephen K Burley
Nucleic acids research 2017:45(D1)
0 Citations (Google Scholar as of 2017-02-15)
Abstract: 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 structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
- The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. [PMID: 25428375]
Peter W Rose, Andreas Prli?, 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, Helen M Berman, Philip E Bourne, Stephen K Burley
Nucleic acids research 2015:43(Database issue)
167 Citations (Google Scholar as of 2017-02-15)
Abstract: 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 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. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
- RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. [PMID: 25183487]
Gregory B Quinn, Chunxiao Bi, Cole H Christie, Kyle Pang, Andreas Prli?, Takanori Nakane, Christine Zardecki, Maria Voigt, Helen M Berman, Philip E Bourne, Peter W Rose
Bioinformatics (Oxford, England) 2015:31(1)
5 Citations (Google Scholar as of 2017-02-15)
Abstract: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service. RCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org). © The Author 2014. Published by Oxford University Press.
- The RCSB Protein Data Bank: new resources for research and education. [PMID: 23193259]
Peter W Rose, Chunxiao Bi, Wolfgang F Bluhm, Cole H Christie, Dimitris Dimitropoulos, Shuchismita Dutta, Rachel K Green, David S Goodsell, Andreas Prlic, Martha Quesada, Gregory B Quinn, Alexander G Ramos, John D Westbrook, Jasmine Young, Christine Zardecki, Helen M Berman, Philip E Bourne
Nucleic acids research 2013:41(Database issue)
288 Citations (Google Scholar as of 2017-02-15)
Abstract: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher's PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.
- The RCSB Protein Data Bank: redesigned web site and web services. [PMID: 21036868]
Peter W Rose, Bojan Beran, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, David S Goodsell, Andreas Prlic, Martha Quesada, Gregory B Quinn, John D Westbrook, Jasmine Young, Benjamin Yukich, Christine Zardecki, Helen M Berman, Philip E Bourne
Nucleic acids research 2011:39(Database issue)
393 Citations (Google Scholar as of 2017-02-15)
Abstract: 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. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural 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. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.