Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server
Heping Zheng,Mahendra D. Chordia,David R. Cooper,Maksymilian Chruszcz,Maksymilian Chruszcz,Peter Müller,George M. Sheldrick,Wladek Minor +7 more
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TLDR
The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal-binding sites, as well as how it can alert researchers to potential errors in metal assignment.Abstract:
Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web serverread more
Citations
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Structural basis for microRNA targeting.
TL;DR: In this paper, the crystal structures of human Argonaute-2 (Ago2) bound to a defined guide RNA with and without target RNAs representing miRNA recognition sites were determined.
Journal ArticleDOI
CheckMyMetal: a macromolecular metal-binding validation tool.
Heping Zheng,David R. Cooper,Przemyslaw J. Porebski,Ivan G. Shabalin,Katarzyna B. Handing,Wladek Minor +5 more
TL;DR: The metal-site validation tool CheckMyMetal is described, with examples to follow.
Journal ArticleDOI
Discovery of a proteinaceous cellular receptor for a norovirus
Robert C. Orchard,Craig B. Wilen,John G. Doench,Megan T. Baldridge,Broc T. McCune,Ying Chiang J. Lee,Sanghyun Lee,Shondra M. Pruett-Miller,Christopher A. Nelson,Daved H. Fremont,Herbert W. Virgin +10 more
TL;DR: Host molecules that are essential for murine NoV (MNoV)–induced cell death are identified, including CD300lf as a proteinaceous receptor, which is essential for MNoV binding and replication in cell lines and primary cells.
Journal ArticleDOI
A public database of macromolecular diffraction experiments.
Marek Grabowski,Karol M. Langner,Marcin Cymborowski,Przemyslaw J. Porebski,Przemyslaw J. Porebski,Piotr Sroka,Heping Zheng,David R. Cooper,Zimmerman,Marc André Elsliger,Stephen K. Burley,Stephen K. Burley,Wladek Minor +12 more
TL;DR: The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.
Journal ArticleDOI
Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis.
Wanatchaporn Arunmanee,M. Pathania,Alexandra S. Solovyova,Le, Brun, Ap,Helen Ridley,Arnaud Baslé,van den Berg B,Jeremy H. Lakey +7 more
TL;DR: Specific LPS binding sites are revealed on OM porin proteins that allow them to stabilize, rather than disrupt, the ordered network of LPS molecules, and it is demonstrated that one such site is essential for porin assembly in the OM.
References
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A short history of SHELX
TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
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UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F. Pettersen,Thomas D. Goddard,Conrad C. Huang,Gregory S. Couch,Daniel M. Greenblatt,Elaine C. Meng,Thomas E. Ferrin +6 more
TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
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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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PROCHECK: a program to check the stereochemical quality of protein structures
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
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Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more