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Daniel R. Roe, Ph. D. - Publications

Affiliations: 
2016- NHLBI National Institutes of Health, Bethesda, MD 
Area:
molecular dynamics, data analysis, enhanced sampling, implicit solvent models
Website:
https://www.lobos.nih.gov/hpcs-droe.shtml
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28 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Love O, Galindo-Murillo R, Roe DR, Dans PD, Cheatham Iii TE, Bergonzo C. modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields. Journal of Chemical Theory and Computation. PMID 39468889 DOI: 10.1021/acs.jctc.4c01164  0.692
2024 Chen L, Roe DR, Kochert M, Simmerling C, Miranda-Quintana RA. k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 20: 5583-5597. PMID 38905589 DOI: 10.1021/acs.jctc.4c00308  0.592
2024 Chen L, Roe DR, Kochert M, Simmerling C, Miranda-Quintana RA. k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations. Biorxiv : the Preprint Server For Biology. PMID 38496504 DOI: 10.1101/2024.03.07.583975  0.592
2023 Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, ... ... Roe DR, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153  0.573
2022 Roe DR, Brooks BR. Quantifying the Effects of Lossy Compression on Energies Calculated from Molecular Dynamics Trajectories. Protein Science : a Publication of the Protein Society. e4511. PMID 36382864 DOI: 10.1002/pro.4511  0.348
2022 Roe DR, Bergonzo C. prepareforleap: An automated tool for fast PDB-to-parameter generation. Journal of Computational Chemistry. 43: 930-935. PMID 35318701 DOI: 10.1002/jcc.26847  0.681
2021 Chen L, Cruz A, Roe DR, Simmonett AC, Wickstrom L, Deng N, Kurtzman T. Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory. Journal of Chemical Theory and Computation. PMID 33830762 DOI: 10.1021/acs.jctc.0c01185  0.681
2020 Roe DR, Brooks BR. A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations. The Journal of Chemical Physics. 153: 054123. PMID 32770927 DOI: 10.1063/5.0013849  0.384
2018 Grossfield A, Patrone PN, Roe DR, Schultz AJ, Siderius DW, Zuckerman DM. Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 1. PMID 30533602  0.404
2018 Roe DR, Cheatham TE. Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. Journal of Computational Chemistry. 39: 2110-2117. PMID 30368859 DOI: 10.1002/Jcc.25382  0.302
2016 Hayatshahi HS, Roe DR, Galindo-Murillo R, Hall KB, Cheatham TE. Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in the GTPase-Associating Center RNA. The Journal of Physical Chemistry. B. PMID 27983843 DOI: 10.1021/Acs.Jpcb.6B08764  0.331
2016 Heidari Z, Roe DR, Galindo-Murillo R, Ghasemi JB, Cheatham TE. Using Wavelet Analysis to Assist in Identification of Significant Events in Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. PMID 27286268 DOI: 10.1021/Acs.Jcim.5B00727  0.392
2015 Thibault JC, Roe DR, Eilbeck K, Cheatham Iii TE, Facelli JC. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. Sar and Qsar in Environmental Research. 26: 577-93. PMID 26387907 DOI: 10.1080/1062936X.2015.1076515  0.465
2015 Bergonzo C, Henriksen NM, Roe DR, Cheatham TE. Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields. Rna (New York, N.Y.). 21: 1578-90. PMID 26124199 DOI: 10.1261/Rna.051102.115  0.713
2015 Galindo-Murillo R, Roe DR, Cheatham TE. Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochimica Et Biophysica Acta. 1850: 1041-58. PMID 25219455 DOI: 10.1016/J.Bbagen.2014.09.007  0.429
2015 Cheatham TE, Roe DR. The impact of heterogeneous computing on workflows for biomolecular simulation and analysis Computing in Science and Engineering. 17: 30-39. DOI: 10.1109/Mcse.2015.7  0.472
2014 Roe DR, Bergonzo C, Cheatham TE. Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods. The Journal of Physical Chemistry. B. 118: 3543-52. PMID 24625009 DOI: 10.1021/Jp4125099  0.705
2014 Thibault JC, Roe DR, Facelli JC, Cheatham TE. Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. Journal of Cheminformatics. 6: 4. PMID 24484917 DOI: 10.1186/1758-2946-6-4  0.39
2014 Bergonzo C, Henriksen NM, Roe DR, Swails JM, Roitberg AE, Cheatham TE. Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide. Journal of Chemical Theory and Computation. 10: 492-499. PMID 24453949 DOI: 10.1021/Ct400862K  0.723
2013 Roe DR, Cheatham TE. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. Journal of Chemical Theory and Computation. 9: 3084-95. PMID 26583988 DOI: 10.1021/Ct400341P  0.358
2013 Nguyen H, Roe DR, Simmerling C. Improved Generalized Born Solvent Model Parameters for Protein Simulations. Journal of Chemical Theory and Computation. 9: 2020-2034. PMID 25788871 DOI: 10.1021/Ct3010485  0.671
2013 Henriksen NM, Roe DR, Cheatham TE. Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations. The Journal of Physical Chemistry. B. 117: 4014-27. PMID 23477537 DOI: 10.1021/Jp400530E  0.552
2012 Brozell SR, Mukherjee S, Balius TE, Roe DR, Case DA, Rizzo RC. Evaluation of DOCK 6 as a pose generation and database enrichment tool. Journal of Computer-Aided Molecular Design. 26: 749-73. PMID 22569593 DOI: 10.1007/S10822-012-9565-Y  0.342
2010 Luchko T, Gusarov S, Roe DR, Simmerling C, Case DA, Tuszynski J, Kovalenko A. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. Journal of Chemical Theory and Computation. 6: 607-624. PMID 20440377 DOI: 10.1021/Ct900460M  0.665
2009 Roe DR, Chaka AM. Structural basis of pathway-dependent force profiles in stretched DNA. The Journal of Physical Chemistry. B. 113: 15364-71. PMID 19845321 DOI: 10.1021/Jp906749J  0.367
2007 Okur A, Roe DR, Cui G, Hornak V, Simmerling C. Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir. Journal of Chemical Theory and Computation. 3: 557-68. PMID 26637035 DOI: 10.1021/ct600263e  0.734
2007 Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. The Journal of Physical Chemistry. B. 111: 1846-57. PMID 17256983 DOI: 10.1021/Jp066831U  0.721
2005 Roe DR, Hornak V, Simmerling C. Folding cooperativity in a three-stranded beta-sheet model. Journal of Molecular Biology. 352: 370-81. PMID 16095612 DOI: 10.1016/J.Jmb.2005.07.036  0.647
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