Structures of large RNA molecules and their complexes
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[1] Vincent B. Chen,et al. KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program , 2009, Protein science : a publication of the Protein Society.
[2] Shuren Wang,et al. A test of enhancing model accuracy in high-throughput crystallography , 2005, Journal of Structural and Functional Genomics.
[3] Krista Joosten,et al. PDB_REDO: constructive validation, more than just looking for errors , 2012, Acta crystallographica. Section D, Biological crystallography.
[4] Daniel Svozil,et al. DNA conformations and their sequence preferences , 2008, Nucleic acids research.
[5] T. Steitz,et al. The kink‐turn: a new RNA secondary structure motif , 2001, The EMBO journal.
[6] Rhiju Das,et al. Correcting pervasive errors in RNA crystallography through enumerative structure prediction , 2011, Nature Methods.
[7] Anna Marie Pyle,et al. RCrane: semi-automated RNA model building , 2012, Acta crystallographica. Section D, Biological crystallography.
[8] Randy J. Read,et al. Crystallography: Crystallographic evidence for deviating C3b structure , 2007, Nature.
[9] M. Rodnina,et al. The crystal structure of unmodified tRNAPhe from Escherichia coli , 2010, Nucleic acids research.
[10] Randy J. Read,et al. Automated identification of elemental ions in macromolecular crystal structures , 2014, Acta crystallographica. Section D, Biological crystallography.
[11] T. Steitz,et al. Crystal structure of the ribosomal RNA domain essential for binding elongation factors. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[12] Shigeyuki Yokoyama,et al. ATP binding by glutamyl‐tRNA synthetase is switched to the productive mode by tRNA binding , 2003, The EMBO journal.
[13] T. Yeates,et al. [22] Detecting and overcoming crystal twinning. , 1997, Methods in enzymology.
[14] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[15] Helen M Berman,et al. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). , 2008, RNA.
[16] A. Brunger. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .
[17] Randy J. Read,et al. Phenix - a comprehensive python-based system for macromolecular structure solution , 2012 .
[18] R. Read. Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors , 1986 .
[19] E. Westhof,et al. Geometric nomenclature and classification of RNA base pairs. , 2001, RNA.
[20] Jennifer A. Doudna,et al. New tools provide a second look at HDV ribozyme structure, dynamics and cleavage , 2014, Nucleic acids research.
[21] Wolfram Saenger,et al. Principles of Nucleic Acid Structure , 1983 .
[22] J. Zou,et al. Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.
[23] T. A. Jones,et al. The Uppsala Electron-Density Server. , 2004, Acta crystallographica. Section D, Biological crystallography.
[24] J. Williamson. Induced fit in RNA–protein recognition , 2000, Nature Structural Biology.
[25] Vincent B. Chen,et al. Correspondence e-mail: , 2000 .
[26] Jayodita C. Sanghvi,et al. Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme , 2007, Nucleic acids research.
[27] J. Richardson,et al. Doing molecular biophysics: finding, naming, and picturing signal within complexity. , 2013, Annual review of biophysics.
[28] Eric Westhof,et al. Frequency and isostericity of RNA base pairs , 2009, Nucleic acids research.
[29] W. B. Arendall,et al. RNA backbone is rotameric , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[30] Y. Chan,et al. The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure. , 2003, Nucleic acids research.
[31] Saulius Gražulis,et al. Crystallography Open Database – an open-access collection of crystal structures , 2009, Journal of applied crystallography.
[32] R. Micura,et al. Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site. , 2008, Angewandte Chemie.
[33] Sameer Velankar,et al. Implementing an X-ray validation pipeline for the Protein Data Bank , 2012, Acta crystallographica. Section D, Biological crystallography.
[34] A. Ferré-D’Amaré,et al. Small self-cleaving ribozymes. , 2010, Cold Spring Harbor perspectives in biology.
[35] Haruki Nakamura,et al. Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.
[36] Paul D Adams,et al. Electronic Reprint Biological Crystallography Electronic Ligand Builder and Optimization Workbench (elbow ): a Tool for Ligand Coordinate and Restraint Generation Biological Crystallography Electronic Ligand Builder and Optimization Workbench (elbow): a Tool for Ligand Coordinate and Restraint Gener , 2022 .
[37] D. Baker,et al. Refinement of protein structures into low-resolution density maps using rosetta. , 2009, Journal of molecular biology.
[38] R. Montange,et al. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine , 2004, Nature.
[39] Hani S. Zaher,et al. The 2′‐OH group of the peptidyl‐tRNA stabilizes an active conformation of the ribosomal PTC , 2011, The EMBO journal.
[40] David Baker,et al. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. , 2013, Annual review of biophysics.
[41] J. Richardson,et al. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. , 1999, Journal of molecular biology.
[42] P. Emsley,et al. Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.
[43] Gregor Blaha,et al. Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. , 2008, Journal of molecular biology.
[44] Vincent B. Chen,et al. Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding , 2011, Science.
[45] F. Major,et al. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data , 2008, Nature.
[46] J. McCloskey,et al. Conformational flexibility in RNA: the role of dihydrouridine. , 1996, Nucleic acids research.
[47] F. Allen. The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.
[48] Daniel N. Wilson,et al. The role of 23S ribosomal RNA residue A2451 in peptide bond synthesis revealed by atomic mutagenesis. , 2008, Chemistry & biology.
[49] M. Zalis,et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. , 1999, Journal of molecular biology.
[50] Randy J. Read,et al. A New Generation of Crystallographic Validation Tools for the Protein Data Bank , 2011, Structure.
[51] D. Baker,et al. Automated de novo prediction of native-like RNA tertiary structures , 2007, Proceedings of the National Academy of Sciences.
[52] A. Ferré-D’Amaré,et al. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein , 2014, Nature Structural &Molecular Biology.
[53] Jack Snoeyink,et al. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone , 2007, Journal of mathematical biology.
[54] A. Ferré-D’Amaré,et al. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. , 2006, Structure.
[55] Randy J. Read,et al. Graphical tools for macromolecular crystallography in PHENIX , 2012, Journal of applied crystallography.
[56] A. Pyle,et al. Stepping through an RNA structure: A novel approach to conformational analysis. , 1998, Journal of molecular biology.
[57] Jennifer A. Doudna,et al. A conformational switch controls hepatitis delta virus ribozyme catalysis , 2004, Nature.