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Items: 1 to 20 of 127

1.

Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions.

Yildirim I, Stern HA, Tubbs JD, Kennedy SD, Turner DH.

J Phys Chem B. 2011 Jul 28;115(29):9261-70. doi: 10.1021/jp2016006. Epub 2011 Jul 1.

2.

The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics.

Tubbs JD, Condon DE, Kennedy SD, Hauser M, Bevilacqua PC, Turner DH.

Biochemistry. 2013 Feb 12;52(6):996-1010. doi: 10.1021/bi3010347. Epub 2013 Jan 29. Erratum in: Biochemistry. 2013 May 14;52(19):3390-2.

3.

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

Yildirim I, Stern HA, Kennedy SD, Tubbs JD, Turner DH.

J Chem Theory Comput. 2010 May 11;6(5):1520-1531. Epub 2010 Apr 16.

4.

Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU).

Condon DE, Yildirim I, Kennedy SD, Mort BC, Kierzek R, Turner DH.

J Phys Chem B. 2014 Feb 6;118(5):1216-28. doi: 10.1021/jp408909t. Epub 2014 Jan 24.

5.

RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case.

Beckman RA, Moreland D, Louise-May S, Humblet C.

J Comput Aided Mol Des. 2006 May;20(5):263-79. Epub 2006 Sep 28.

PMID:
17006738
6.

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.

Bergonzo C, Henriksen NM, Roe DR, Cheatham TE 3rd.

RNA. 2015 Sep;21(9):1578-90. doi: 10.1261/rna.051102.115. Epub 2015 Jun 29.

7.

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs.

Yildirim I, Kennedy SD, Stern HA, Hart JM, Kierzek R, Turner DH.

J Chem Theory Comput. 2012 Jan 10;8(1):172-181. Epub 2011 Dec 1.

8.

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

Ditzler MA, Otyepka M, Sponer J, Walter NG.

Acc Chem Res. 2010 Jan 19;43(1):40-7. doi: 10.1021/ar900093g.

9.

Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations.

Schrodt MV, Andrews CT, Elcock AH.

J Chem Theory Comput. 2015 Dec 8;11(12):5906-17. doi: 10.1021/acs.jctc.5b00899. Epub 2015 Nov 18.

10.

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.

Aliev AE, Courtier-Murias D.

J Phys Chem B. 2010 Sep 30;114(38):12358-75. doi: 10.1021/jp101581h. Erratum in: J Phys Chem B. 2012 Jul 12;116(27):7996.

PMID:
20825228
11.

Improved Force Field Parameters Lead to a Better Description of RNA Structure.

Bergonzo C, Cheatham TE 3rd.

J Chem Theory Comput. 2015 Sep 8;11(9):3969-72. doi: 10.1021/acs.jctc.5b00444. Epub 2015 Aug 18.

PMID:
26575892
12.

Free energy profile of RNA hairpins: a molecular dynamics simulation study.

Deng NJ, Cieplak P.

Biophys J. 2010 Feb 17;98(4):627-36. doi: 10.1016/j.bpj.2009.10.040.

13.

Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field.

Wales DJ, Yildirim I.

J Phys Chem B. 2017 Apr 13;121(14):2989-2999. doi: 10.1021/acs.jpcb.7b00819. Epub 2017 Mar 31.

PMID:
28319659
14.

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin.

Giambaşu GM, York DM, Case DA.

RNA. 2015 May;21(5):963-74. doi: 10.1261/rna.047357.114. Epub 2015 Mar 24.

15.
17.

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.

Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J.

J Phys Chem B. 2015 Dec 10;119(49):15176-90. doi: 10.1021/acs.jpcb.5b08876. Epub 2015 Nov 30.

PMID:
26548477
18.

Assessing the Current State of Amber Force Field Modifications for DNA.

Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurečka P, Cheatham TE 3rd.

J Chem Theory Comput. 2016 Aug 9;12(8):4114-27. doi: 10.1021/acs.jctc.6b00186. Epub 2016 Jul 7.

19.

Disagreement Between the Structure of the dTpT Thymine Pair Determined by NMR and Molecular Dynamics Simulations Using Amber 14 Force Fields.

Nganou C, Kennedy SD, McCamant DW.

J Phys Chem B. 2016 Feb 25;120(7):1250-8. doi: 10.1021/acs.jpcb.6b00191. Epub 2016 Feb 17.

PMID:
26836489
20.

Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results.

Yildirim I, Kierzek E, Kierzek R, Schatz GC.

J Phys Chem B. 2014 Dec 11;118(49):14177-87. doi: 10.1021/jp506703g. Epub 2014 Sep 30.

PMID:
25268896

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