Turning limited experimental information into 3D models of RNA.

RNA
Samuel Coulbourn Flores, Russ B Altman

Abstract

Our understanding of RNA functions in the cell is evolving rapidly. As for proteins, the detailed three-dimensional (3D) structure of RNA is often key to understanding its function. Although crystallography and nuclear magnetic resonance (NMR) can determine the atomic coordinates of some RNA structures, many 3D structures present technical challenges that make these methods difficult to apply. The great flexibility of RNA, its charged backbone, dearth of specific surface features, and propensity for kinetic traps all conspire with its long folding time, to challenge in silico methods for physics-based folding. On the other hand, base-pairing interactions (either in runs to form helices or isolated tertiary contacts) and motifs are often available from relatively low-cost experiments or informatics analyses. We present RNABuilder, a novel code that uses internal coordinate mechanics to satisfy user-specified base pairing and steric forces under chemical constraints. The code recapitulates the topology and characteristic L-shape of tRNA and obtains an accurate noncrystallographic structure of the Tetrahymena ribozyme P4/P6 domain. The algorithm scales nearly linearly with molecule size, opening the door to the modeling of signifi...Continue Reading

References

Aug 25, 1978·Journal of Molecular Biology·J L SussmanS H Kim
Aug 16, 1974·Nature·J D RobertusA Klug
Jan 1, 1966·Cold Spring Harbor Symposia on Quantitative Biology·J T MadisonH K Kung
Jan 1, 1966·Cold Spring Harbor Symposia on Quantitative Biology·U L RajBhandaryH G Khorana
Aug 19, 1967·Nature·W Fuller, A Hodgson
Apr 21, 1995·Journal of Molecular Biology·D GautheretR R Gutell
Feb 20, 1993·Journal of Molecular Biology·D GautheretR Cedergren
Feb 11, 1994·Journal of Molecular Biology·F L Murphy, T R Cech
Oct 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·F MajorR Cedergren
Sep 20, 1996·Science·J H CateJ A Doudna
Dec 6, 1996·Science·R J Stern, M G Abdelsalam
Oct 23, 1998·Nature·A R Ferré-D'AmaréJ A Doudna
Aug 24, 1999·Angewandte Chemie·R T BateyJ A Doudna
Jul 25, 2000·Biochemical and Biophysical Research Communications·Y IkawaT Inoue
Apr 11, 2001·Proceedings of the National Academy of Sciences of the United States of America·P NissenT A Steitz
Aug 15, 2002·Nucleic Acids Research·Neocles B LeontisEric Westhof
Nov 8, 2002·Nature·Christopher D SnowMartin Gruebele
Jun 26, 2003·Nucleic Acids Research·Huanwang YangEric Westhof
Mar 19, 1965·Science·R W HOLLEYA ZAMIR
Jul 9, 2005·Journal of Molecular Biology·Jared H DavisSamuel E Butcher
Dec 24, 2005·RNA·Aurélie Lescoute, Eric Westhof
Mar 7, 2007·RNA·Alain LaederachRuss B Altman
May 18, 2007·RNA·Rahul Tyagi, David H Mathews
Aug 30, 2007·Proceedings of the National Academy of Sciences of the United States of America·Rhiju Das, David Baker
May 13, 1983·Science·S KirkpatrickM P Vecchi
Mar 7, 2008·Nature·Marc Parisien, François Major
Jun 30, 2009·FEBS Letters·Asamoah Nkwanta, Wilfred Ndifon
Jun 15, 2010·Journal of Molecular Biology·Yaqi WanDaniel Herschlag

❮ Previous
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Citations

Sep 15, 2014·The Journal of Chemical Physics·Ya-Zhou ShiZhi-Jie Tan
Nov 15, 2011·Journal of the American Medical Informatics Association : JAMIA·Scott L DelpRuss B Altman
Feb 15, 2011·Proceedings of the National Academy of Sciences of the United States of America·Adelene Y L Sim, Michael Levitt
Mar 19, 2011·The Journal of Physical Chemistry. B·Song Cao, Shi-Jie Chen
Nov 11, 2011·Journal of the American Chemical Society·Erich G Chapman, Victoria J DeRose
Jun 22, 2012·Nucleic Acids Research·Euripedes de Almeida RibeiroKristina Djinović-Carugo
Sep 8, 2011·Briefings in Bioinformatics·Magdalena RotherJanusz M Bujnicki
Jan 10, 2012·Briefings in Bioinformatics·Samuel C FloresXuhui Huang
Apr 28, 2012·Nucleic Acids Research·Mariusz PopendaRyszard W Adamiak
Jun 23, 2012·Science·Petter HammarJohan Elf
Apr 28, 2012·Current Opinion in Structural Biology·Adelene Y L SimMichael Levitt
Dec 18, 2015·Nucleic Acids Research·Alex TekSamuel Coulbourn Flores
Oct 21, 2015·Nucleic Acids Research·Anthony M MustoeCharles L Brooks
Dec 15, 2015·Journal of Molecular Graphics & Modelling·Rico Beier, Dirk Labudde
Apr 19, 2011·Current Opinion in Structural Biology·Maximillian H BailorHashim M Al-Hashimi
Nov 21, 2015·Journal of Molecular Biology·Srinivas Somarowthu
Mar 27, 2016·Methods : a Companion to Methods in Enzymology·Marcin BiesiadaKatarzyna J Purzycka
Jul 23, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Samuel Coulbourn FloresRuss Biagio Altman
Nov 18, 2015·Journal of Chemical Theory and Computation·Tristan CragnoliniSamuela Pasquali
Dec 27, 2012·Methods : a Companion to Methods in Enzymology·Ezgi Karaca, Alexandre M J J Bonvin
Oct 3, 2013·Methods : a Companion to Methods in Enzymology·Irina TuszynskaJanusz M Bujnicki
Nov 13, 2012·PloS One·Liang Liu, Shi-Jie Chen
Nov 6, 2013·Acta Crystallographica. Section D, Biological Crystallography·Marco MarciaAnna Marie Pyle
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Adelene Y L SimJulie Bernauer
Dec 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Parin SripakdeevongRhiju Das
Aug 6, 2016·PLoS Computational Biology·Jun LiWei Wang
Aug 9, 2018·Physical Chemistry Chemical Physics : PCCP·Antarip HalderAbhijit Mitra
Nov 23, 2019·Biomolecules·Thomas CaulfieldSamuel Coulbourn Flores
May 21, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Tristan CragnoliniSamuela Pasquali
Nov 7, 2017·PLoS Computational Biology·Michael F Sloma, David H Mathews
May 16, 2019·Annual Review of Biophysics·Eike-Christian WamhoffMark Bathe
Sep 3, 2020·Acta Crystallographica. Section D, Structural Biology·Jiří ČernýBohdan Schneider
Jan 1, 2012·ISRN Bioinformatics·Debra KnisleyAlissa Rockney
Nov 17, 2020·Frontiers in Genetics·Bing LiZhichao Miao
Apr 3, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Jian ZhangWei Wang

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