Benjamin T. Yukich

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

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.

Integration of open access literature into the RCSB Protein Data Bank using BioLit

BackgroundBiological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright restriction, this distinction between database and literature is blurring. To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB).ResultsBioLit provides an enhanced view of articles with markup of semantic data and links to biological databases, based on the content of the article. For example, words matching to existing biological ontologies are highlighted and database identifiers are linked to their database of origin. Among other functions, it identifies PDB IDs that are mentioned in the open access literature, by parsing the full text for all research articles in PubMed Central (PMC) and exposing the results as simple XML Web Services. Here, we integrate BioLit results with the RCSB PDB website by using these services to find PDB IDs that are mentioned in research articles and subsequently retrieving abstract, figures, and text excerpts for those articles. A new RCSB PDB literature view permits browsing through the figures and abstracts of the articles that mention a given structure. The BioLit Web Services that are providing the underlying data are publicly accessible. A client library is provided that supports querying these services (Java).ConclusionsThe integration between literature and websites, as demonstrated here with the RCSB PDB, provides a broader view for how a given structure has been analyzed and used. This approach detects the mention of a PDB structure even if it is not formally cited in the paper. Other structures related through the same literature references can also be identified, possibly providing new scientific insight. To our knowledge this is the first time that database and literature have been integrated in this way and it speaks to the opportunities afforded by open and free access to both database and literature content.

Will Widgets and Semantic Tagging Change Computational Biology

We argue here, through the use of several examples from our work in support of structural biology, that the answer to the question posed by the title of this Perspective is a resounding yes. The discussion that follows is aimed primarily at those of the journals readers who are biological resource developers and Web page developers interested in developing the richest possible Web pages. However, those of you who simply use biological resources might find this a helpful discussion in understanding what is on the horizon. Whatever your interest, please let us hear your opinion on the question posed by this Perspective through the associated comment feature.

The evolution of the RCSB Protein Data Bank website

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education by providing an essential resource of information about biomolecular structures. As a member of the Worldwide Protein Data Bank (wwPDB), the RCSB PDB curates and annotates the data about the experimentally determined three‐dimensional structures of proteins and nucleic acids that are deposited into the PDB archive. The RCSB PDB also provides online resources to access the data in the archive, including a relational database supporting simple and complex query and reporting, visualization tools, structure‐sequence comparison tools, access to the associated literature, and educational services. In the 11 years (1999–2010) since RCSB PDB has been in operation, the amount of data in the archive has increased six‐fold, along with an increase in the complexity of structures being determined and in the number of experimental methods used. The evolution required by RCSB PDB to meet these challenges provides insight into the motivation and challenges of developing and maintaining a major biological resource, particularly the one used in understanding the molecular details of living systems in both normal and disease states.

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

The RCSB Protein Data Bank (RCSB PDB, www.pdb.org) is a key online resource for structural biology and related scientific disciplines. The website is used on average by 165 000 unique visitors per month, and more than 2000 other websites link to it. The amount and complexity of PDB data as well as the expectations on its usage are growing rapidly. Therefore, ensuring the reliability and robustness of the RCSB PDB query and distribution systems are crucially important and increasingly challenging. This article describes quality assurance for the RCSB PDB website at several distinct levels, including: (i) hardware redundancy and failover, (ii) testing protocols for weekly database updates, (iii) testing and release procedures for major software updates and (iv) miscellaneous monitoring and troubleshooting tools and practices. As such it provides suggestions for how other websites might be operated. Database URL: www.pdb.org

Suppression of Hidden Order and Emergence of Ferromagnetism in URu 2-x Re x Si 2

Measurements on URu 2-x Re x Si 2 single crystals indicate that substitution of Re for Ru in URu 2 Si 2 reduces the transition temperature of the hidden order state and quickly destroys superconductivity. At intermediate Re concentrations, weak ferromagnetism emerges and non Fermi liquid (NFL) behavior is observed in the low-temperature specific heat and electrical resistivity. A scaled Arrott analysis of the magnetization indicates the onset of ferromagnetism at x =0.15, where the hidden order disappears, and that the quantum phase transition is associated with novel critical exponents.

Evolution of Superconducting and Hidden Order Phases in URu2Si2 Under Applied Pressure

Electrical resistivity measurements performed under applied hydrostatic pressure and in magnetic fields have been used to probe the hidden order (HO) and superconducting (SC) states of URu{sub 2}Si{sub 2}, which have ambient-pressure transition temperatures T{sub 0} = 17.5 K and T{sub c} = 1.5 K, respectively. T{sub 0} increases with applied pressure and a distinct kink in its pressure dependence is observed at 15 kbar; this feature is associated with the onset of antiferromagnetism. The pressure dependence of the SC upper critical field has been measured with the external field aligned parallel to both crystalline axes. The SC phase is smoothly suppressed to a critical pressure of about 15 kbar and no qualitative change in the critical field curves is observed. The co-evolution of the HO and SC phases is discussed within the context of a model in which the two phases compete for Fermi surface fraction. (authors)

Tuning of Hidden Order and Superconductivity in URu2Si2 by Applied Pressure and Re Substitution

Single crystals of URu2-xRexSi2 have been grown via the Czochralski technique. Detailed electrical transport studies under pressure on single crystals of URu2Si2 confirm that the zero- temperature critical field is suppressed smoothly towards an extrapolated critical pressure of 15 kbar, which also corresponds to the accepted critical pressure of the hidden order phase. Improving on previous work on polycrystalline samples, studies of single crystals of URu2-xRexSi2 have provided more precise tracking of the suppression of both the hidden order phase at low doping and the ferromagnetic phase at intermediate Re concentrations.