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Journal of Cheminformatics|February 4, 2014
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharingJulien C Thibault, Daniel R Roe, Julio C Facelli, et al.Journal of Chemical Information and Modeling|February 19, 2013
iBIOMES: managing and sharing biomolecular simulation data in a distributed environmentJulien C Thibault, Julio C Facelli, Thomas E CheathamJournal of Chemical Information and Modeling|May 17, 2014
iBIOMES Lite: summarizing biomolecular simulation data in limited settingsJulien C Thibault, Thomas E Cheatham, Julio C FacelliJournal of Chemical Theory and Computation|November 20, 2015
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory DataDaniel R Roe, Thomas E CheathamJournal of Computational Chemistry|October 29, 2018
Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory dataDaniel R Roe, Thomas E CheathamThe Journal of Physical Chemistry. B|March 15, 2014
Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methodsDaniel R Roe, Christina Bergonzo, Thomas E CheathamBiochimica Et Biophysica Acta|September 16, 2014
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)Rodrigo Galindo-Murillo, Daniel R Roe, Thomas E CheathamThe Journal of Physical Chemistry. B|March 13, 2013
Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulationsNiel M Henriksen, Daniel R Roe, Thomas E CheathamNature Communications|October 30, 2014
On the absence of intrahelical DNA dynamics on the μs to ms timescaleRodrigo Galindo-Murillo, Daniel R Roe, Thomas E CheathamRNA (New York, N.Y.)|July 1, 2015
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fieldsChristina Bergonzo, Niel M Henriksen, Daniel R Roe, et al.Pageof 25