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Journal of Biomolecular Structure and Dynamics Volume 24, 2007 - Issue 5
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Original Articles

Molecular Dynamics Simulation for Probing the Flexibility of the 35 Nucleotide SL1 Sequence Kissing Complex from HIV-1Lai Genomic RNA

Sonia Mazier Centre de Biophysique Moléculaire UPR no 4301 du CNRS, affiliated to the University of Orléans and to INSERM, CNRS—Rue Charles Sadron, 45071, Orléans cedex 2, France
&
Daniel Genest Centre de Biophysique Moléculaire UPR no 4301 du CNRS, affiliated to the University of Orléans and to INSERM, CNRS—Rue Charles Sadron, 45071, Orléans cedex 2, France
Pages 471-479 | Received 02 Nov 2006, Published online: 15 May 2012

Citations (7)

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Jian-Ping Hu, Hong-Qiu He, Dian-Yong Tang, Guo-Feng Sun, Yuan-Qin Zhang, Jing Fan & Shan Chang. (2013) Study on the interactions between diketo-acid inhibitors and prototype foamy virus integrase-DNA complex via molecular docking and comparative molecular dynamics simulation methods. Journal of Biomolecular Structure and Dynamics 31:7, pages 734-747.
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Articles from other publishers (6)

Jiří Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Richard A. Cunha, Alejandro Gil-Ley, Giovanni Pinamonti, Simón Poblete, Petr Jurečka, Nils G. Walter & Michal Otyepka. (2018) RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews 118:8, pages 4177-4338.
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Marek Havrila, Marie Zgarbová, Petr Jurečka, Pavel Banáš, Miroslav Krepl, Michal Otyepka & Jiří Šponer. (2015) Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. The Journal of Physical Chemistry B 119:49, pages 15176-15190.
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Loussiné Zargarian, Igor Kanevsky, Ali Bazzi, Jonathan Boynard, Françoise Chaminade, Philippe Fossé & Olivier Mauffret. (2009) Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin. Nucleic Acids Research 37:12, pages 4043-4054.
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Joanna Sarzyńska, Kamila Réblová, Jiří Šponer & Tadeusz Kuliński. (2008) Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics. Biopolymers 89:9, pages 732-746.
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Sonia Mazier & Daniel Genest. (2008) Insight into the intrinsic flexibility of the SL1 stem-loop from genomic RNA of HIV-1 as probed by molecular dynamics simulation. Biopolymers 89:3, pages 187-196.
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Kamila Réblová, Eva Fadrná, Joanna Sarzynska, Tadeusz Kulinski, Petr Kulhánek, Eric Ennifar, Jaroslav Koča & Jiří Šponer. (2007) Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics. Biophysical Journal 93:11, pages 3932-3949.
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