Roe DR - Search Results

1

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing.

Thibault JC, Roe DR, Facelli JC, Cheatham TE 3rd. Thibault JC, et al. Among authors: roe dr. J Cheminform. 2014 Jan 30;6(1):4. doi: 10.1186/1758-2946-6-4. J Cheminform. 2014. PMID: 24484917 Free PMC article.

2

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

Henriksen NM, Roe DR, Cheatham TE 3rd. Henriksen NM, et al. Among authors: roe dr. J Phys Chem B. 2013 Apr 18;117(15):4014-27. doi: 10.1021/jp400530e. Epub 2013 Apr 4. J Phys Chem B. 2013. PMID: 23477537 Free PMC article.

3

Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis.

Ashton NN, Roe DR, Weiss RB, Cheatham TE 3rd, Stewart RJ. Ashton NN, et al. Among authors: roe dr. Biomacromolecules. 2013 Oct 14;14(10):3668-81. doi: 10.1021/bm401036z. Epub 2013 Oct 3. Biomacromolecules. 2013. PMID: 24050221

4

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.

Bergonzo C, Henriksen NM, Roe DR, Swails JM, Roitberg AE, Cheatham TE 3rd. Bergonzo C, et al. Among authors: roe dr. J Chem Theory Comput. 2014 Jan 14;10(1):492-499. doi: 10.1021/ct400862k. Epub 2013 Nov 15. J Chem Theory Comput. 2014. PMID: 24453949 Free PMC article.

5

Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

Roe DR, Bergonzo C, Cheatham TE 3rd. Roe DR, et al. J Phys Chem B. 2014 Apr 3;118(13):3543-52. doi: 10.1021/jp4125099. Epub 2014 Mar 25. J Phys Chem B. 2014. PMID: 24625009 Free PMC article.

6

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).

Galindo-Murillo R, Roe DR, Cheatham TE 3rd. Galindo-Murillo R, et al. Among authors: roe dr. Biochim Biophys Acta. 2015 May;1850(5):1041-1058. doi: 10.1016/j.bbagen.2014.09.007. Epub 2014 Sep 16. Biochim Biophys Acta. 2015. PMID: 25219455 Free PMC article.

7

On the absence of intrahelical DNA dynamics on the μs to ms timescale.

Galindo-Murillo R, Roe DR, Cheatham TE 3rd. Galindo-Murillo R, et al. Among authors: roe dr. Nat Commun. 2014 Oct 29;5:5152. doi: 10.1038/ncomms6152. Nat Commun. 2014. PMID: 25351257 Free PMC article.

8

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

Bergonzo C, Henriksen NM, Roe DR, Cheatham TE 3rd. Bergonzo C, et al. Among authors: roe dr. RNA. 2015 Sep;21(9):1578-90. doi: 10.1261/rna.051102.115. Epub 2015 Jun 29. RNA. 2015. PMID: 26124199 Free PMC article.

9

Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

Thibault JC, Roe DR, Eilbeck K, Cheatham TE III, Facelli JC. Thibault JC, et al. Among authors: roe dr. SAR QSAR Environ Res. 2015;26(7-9):577-93. doi: 10.1080/1062936X.2015.1076515. Epub 2015 Sep 21. SAR QSAR Environ Res. 2015. PMID: 26387907 Free PMC article. Review.

10

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.

Roe DR, Cheatham TE 3rd. Roe DR, et al. J Chem Theory Comput. 2013 Jul 9;9(7):3084-95. doi: 10.1021/ct400341p. Epub 2013 Jun 25. J Chem Theory Comput. 2013. PMID: 26583988

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