Journal ArticleDOI
Calculation of Standard Atomic Volumes for RNA and Comparison with Proteins: RNA is Packed More Tightly
Neil R. Voss,Mark Gerstein +1 more
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TLDR
This work addresses the question of RNA packing using Voronoi volume calculations on a set of high-resolution RNA crystal structures, and finds that RNA bases have similar packing volumes to DNA bases, despite the absence of tertiary contacts in DNA.About:
This article is published in Journal of Molecular Biology.The article was published on 2005-02-18. It has received 134 citations till now. The article focuses on the topics: RNA & Protein tertiary structure.read more
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ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions
Daniel Franke,Maxim V. Petoukhov,Maxim V. Petoukhov,Peter V. Konarev,Peter V. Konarev,Alejandro Panjkovich,Anne T. Tuukkanen,Haydyn D. T. Mertens,Alexey Kikhney,Nelly R. Hajizadeh,J.M. Franklin,Cy M. Jeffries,Dmitri I. Svergun +12 more
TL;DR: Developments and improvements of the ATSAS software suite for analysis of small-angle scattering data of biological macromolecules or nanoparticles are described.
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3V: cavity, channel and cleft volume calculator and extractor
Neil R. Voss,Mark Gerstein +1 more
TL;DR: The 3V web server can automatically extract and comprehensively analyze all the internal volumes from input RNA and protein structures, and produces volumetric representations, both as images and downloadable files, which can be used for further analysis.
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Small-angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls
David A. Jacques,Jill Trewhella +1 more
TL;DR: This review is intended to provide a road map through the small‐angle scattering experiment, while also providing a set of guidelines for the critical evaluation of scattering data.
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Molecular Basis for Interaction of let-7 MicroRNAs with Lin28.
Yunsun Nam,Casandra Chen,Casandra Chen,Richard I. Gregory,Richard I. Gregory,James J. Chou,Piotr Sliz,Piotr Sliz +7 more
TL;DR: The data provide a molecular explanation for Lin28 specificity and a model for how it regulates let-7, and show by NMR spectroscopy that the linker connecting the two folded domains is flexible, accommodating Lin28 binding to diverseLet-7 family members.
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How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective
TL;DR: The interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins is presented and the different strategies to obtain 3-dimensional models of IDPs, free in solution and associated in a complex are reviewed.
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.
Journal ArticleDOI
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Axel T. Brunger,Axel T. Brunger,Paul D. Adams,G M Clore,W. L. DeLano,Piet Gros,R.W. Grosse-Kunstleve,R.W. Grosse-Kunstleve,Jiansheng Jiang,J. Kuszewski,Michael Nilges,Navraj S. Pannu,Randy J. Read,Luke M. Rice,Thomas Simonson,Gregory L. Warren +15 more
TL;DR: The Crystallography & NMR System (CNS) as mentioned in this paper is a software suite for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy.
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