The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications
John L. Moreland,Apostol Gramada,Oleksandr V Buzko,Qing Zhang,Philip E. Bourne,Philip E. Bourne +5 more
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TLDR
The MBT provides a well-organized assortment of core classes that provide a uniform data model for the description of biological structures and automate most common tasks associated with the development of applications in the molecular sciences.Abstract:
Background
The large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed that offer flexibility, rapid application development and deployment as standalone applications or available through the Web.read more
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Bioaerosols in the Earth system: Climate, health, and ecosystem interactions
Janine Fröhlich-Nowoisky,Christopher J. Kampf,Christopher J. Kampf,Bettina Weber,J. Alex Huffman,Christopher Pöhlker,Meinrat O. Andreae,Naama Lang-Yona,Susannah M. Burrows,Sachin S. Gunthe,W. Elbert,Hang Su,Peter Hoor,Eckhard Thines,Thorsten Hoffmann,Viviane R. Després,Ulrich Pöschl +16 more
TL;DR: A review of the state of bioaerosol research, highlights recent advances, and outlines future perspectives in terms of identification, characterization, transport and transformation processes, as well as their interactions with climate, health, and ecosystems, focusing on the role bio-aerosols play in the Earth system.
Journal ArticleDOI
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,Helen M. Berman,Philip E. Bourne,Stephen K. Burley +14 more
TL;DR: 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 are described.
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The RCSB Protein Data Bank: new resources for research and education
Peter W. Rose,Chunxiao Bi,Wolfgang F. Bluhm,Cole Christie,Dimitris Dimitropoulos,Shuchismita Dutta,Rachel Kramer Green,David S. Goodsell,Andreas Prlić,Martha Quesada,Gregory B. Quinn,Alexander G. Ramos,John D. Westbrook,Jasmine Young,Christine Zardecki,Helen M. Berman,Philip E. Bourne +16 more
TL;DR: Improved methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments enable new opportunities for analyzing and understanding structure data.
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AQP4 antibodies in neuromyelitis optica: diagnostic and pathogenetic relevance
Sven Jarius,Brigitte Wildemann +1 more
TL;DR: The latest evidence in support of a direct involvement of AQP4-Ab in the immunopathogenesis of NMO is summarized, the diagnostic tests currently available for the detection of this serum reactivity are critically appraised and a strong rationale for the use of therapies targeted against B cells or antibodies in the treatment of N MO is provided.
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Lignin-modifying enzymes in filamentous basidiomycetes--ecological, functional and phylogenetic review.
TL;DR: This review gives a current ecological, genomic, and protein functional and phylogenetic perspective of the wood and lignocellulose‐decaying basidiomycetous fungi.
References
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The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
TL;DR: The MOLSCRIPT program as discussed by the authors produces plots of protein structures using several different kinds of representations, including simple wire models, ball-and-stick models, CPK models and text labels.
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SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
Nicolas Guex,Manuel C. Peitsch +1 more
TL;DR: An environment for comparative protein modeling is developed that consists of SWISS‐MODEL, a server for automated comparativeprotein modeling and of the SWiss‐PdbViewer, a sequence to structure workbench that provides a large selection of structure analysis and display tools.