The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the ‘best structures’ for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.
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 macromolecular structure data through the single global archive for such data, the PDB. Similarly, PDBe is a member of the EMDataBank organisation (emdatabank.org), which manages the EMDB archive for electron microscopy data. PDBe also develops tools that help the biomedical science community to make effective use of the data in the PDB and EMDB for their research. Here we describe new or improved services, including updated SIFTS mappings to other bioinformatics resources, a new browser for the PDB archive based on Gene Ontology (GO) annotation, updates to the analysis of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.
IntroductionAlthough lung cancer screening is being implemented in the UK, there is uncertainty about the optimal invitation strategy. Here, we report participation in a community screening programme following a population-based invitation approach, examine factors associated with participation, and compare outcomes with hypothetical targeted invitations.MethodsLetters were sent to all individuals (age 55–80) registered with a general practice (n=35 practices) in North and East Manchester, inviting ever-smokers to attend a Lung Health Check (LHC). Attendees at higher risk (PLCOm2012NoRacescore≥1.5%) were offered two rounds of annual low-dose CT screening. Primary care recorded smoking codes (live and historical) were used to model hypothetical targeted invitation approaches for comparison.ResultsLetters were sent to 35 899 individuals, 71% from the most socioeconomically deprived quintile. Estimated response rate in ever-smokers was 49%; a lower response rate was associated with younger age, male sex, and primary care recorded current smoking status (adjOR 0.55 (95% CI 0.52 to 0.58), p<0.001). 83% of eligible respondents attended an LHC (n=8887/10 708). 51% were eligible for screening (n=4540/8887) of whom 98% had a baseline scan (n=4468/4540). Screening adherence was 83% (n=3488/4199) and lung cancer detection 3.2% (n=144) over 2 rounds. Modelled targeted approaches required 32%–48% fewer invitations, identified 94.6%–99.3% individuals eligible for screening, and included 97.1%–98.6% of screen-detected lung cancers.DiscussionUsing a population-based invitation strategy, in an area of high socioeconomic deprivation, is effective and may increase screening accessibility. Due to limitations in primary care records, targeted approaches should incorporate historical smoking codes and individuals with absent smoking records.
The first study by nmr of the integral membrane protein, the bacterial light‐harvesting (LH) antenna protein LH1β, is reported. The photosynthetic apparatus of purple bacteria contains two different kinds of antenna complexes (LH1 and LH2), which consist of two small integral membrane proteins α and β, each of approximately 6 kDa, and bacteriochlorophyll and carotenoid pigments. We have purified the antenna polypeptide LH1β from Rhodobacter sphaeroides, and have recorded CD spectra and a series of two‐dimensional nmr spectra. A comparison of CD spectra of LH1β observed in organic solvents and detergent micelles shows that the helical character of the peptide does not change appreciably between the two milieus. A significantly high‐field shifted methyl signal was observed both in organic solvents and in detergent micelles, implying that a similar three‐dimensional structure is present in each case. However, the 1H‐nmr signals observed in organic solvents had a narrower line width and better resolution, and it is shown that in this case organic solvents provide a better medium for nmr studies than detergent micelles. A sequential assignment has been carried out on the C‐terminal transmembrane region, which is the region in which the pigment is bound. The region is shown to have a helical structure by the chemical shift values of the α‐CH protons and the presence of nuclear Overhauser effects characteristic of helices. An analysis of the amide proton chemical shifts of the residues surrounding the histidine chlorophyll ligand suggests that the local structure is well ordered even in the absence of protein–lipid and protein–pigment interactions. Its structure was determined from 348 nmr‐derived constraints by using distance geometry calculations. The polypeptide contains an α‐helix extending from Leu19 (position of cytoplasmic surface) to Trp44 (position of periplasmic surface). The helix is bent, as expected from the amide proton chemical shifts, and it is similar to the polypeptide fold of the previously determined crystal structure of Rhodopseudomonas acidophila Ac10050 LH2β (S. M. Prince et al., Journal of Molecular Biology, 1997, Vol. 268, pp. 412–423). It is concluded that the polypeptide conformation of this region may facilitate assembly of the LH complex. © 1999 John Wiley & Sons, Inc. Biopoly 49: 361–372, 1999
LiteMol is a unique and comprehensive macromolecular structure viewer which through real-time data delivery enables even large macromolecular structures to be visualised in the browser in a platform independent manner. LiteMol is fully integrated into the webpages at the Protein Data Bank in Europe (PDBe.org), a founder member of the wwPDB.LiteMol is composed of a 3D molecular viewer LiteMol Viewer, data delivery services CoordinateServer and DensityServer, and a data format called BinaryCIF. LiteMol Viewer provides interactive web-browser based visualisation of 3D structures together with maps and annotation of biological context. CoordinateServer and DensityServer enable a dramatic reduction of data transfer size by sending only what is currently relevant to the user instead of whole files. Finally, the BinaryCIF format provides very high compression ratios while retaining compatibility with existing standards used by the wwPDB consortium. As shown by our benchmarks, it is the fastest 3D viewer currently available.LiteMol is able to display 3D coordinate data in standard representations (cartoons, balls and sticks, etc.) and overlay them with additional annotations (e.g., sequence annotation from Uniprot, annotated assemblies or data quality assessment from wwPDB validation reports) accessed from the PDBe API. Moreover, it readily displays experimental evidence (i.e., electron density maps derived from deposited structure factors for X-ray diffraction data, and electric potential maps for Cryo-EM derived models).LiteMol and its components are freely available for integration into other online services and, in addition to PDBe, it is currently integrated into Glycopedia and integration to UniProt and Open Targets is in progress.LiteMol web pages are available at http://ncbr.muni.cz/LiteMol
The Protein Data Bank (PDB) contains a wealth of structural and functional knowledge about proteins, RNA, DNA, and other macromolecules, and their assemblies and complexes with small molecules. The challenge faced by the providers of PDB data is to make this knowledge accessible to an increasingly large and diverse audience, ranging from expert structural biologists to non-specialist consumers of structural information. Educators, students, and general audiences will have their own specific interests and expectations from molecular structure data. For a general user, a 2D image of hemoglobin illustrates how a protein looks at a microscopic level. For high school students and educators, 3D models or computer graphics can show how one or a few specific proteins can assemble into an icosahedral virus. In contrast, PhD and post-doc level researchers require expert guidance on how to critically assess the quality of structural data, and in-depth training on the use of specialist tools and resources for the comparison and analysis of structures. The PDB archive is managed by members of the Worldwide Protein Data Bank (wwPDB): the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; rcsb.org), Protein Data Bank in Europe (PDBe; pdbe.org), Protein Data Bank Japan (PDBj), and BioMagResBank (BMRB, bmrb.wisc.edu). In addition to managing and distributing structural data, the wwPDB partners are engaged in numerous outreach initiatives and user training programs. These efforts are vital to ensuring that these uniquely valuable data can be effectively accessed and used by research scientists, students, and educators alike. This talk will describe on-going wwPDB outreach efforts and highlight exciting new initiatives at the RCSB PDB, PDBe and PDBj.
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