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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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25/40 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
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  0.577
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  0.353
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  0.68
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  0.386
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  0.411
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  0.338
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  0.388
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  0.464
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  0.711
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  0.431
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  0.473
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  0.707
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  0.386
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  0.721
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  0.679
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  0.557
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  0.34
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  0.668
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  0.376
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  0.731
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  0.709
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  0.655
Low-probability matches (unlikely to be authored by this person)
2013 Ashton NN, Roe DR, Weiss RB, Cheatham TE, Stewart RJ. Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis. Biomacromolecules. 14: 3668-81. PMID 24050221 DOI: 10.1021/Bm401036Z  0.3
2014 Galindo-Murillo R, Roe DR, Cheatham TE. On the absence of intrahelical DNA dynamics on the μs to ms timescale. Nature Communications. 5: 5152. PMID 25351257 DOI: 10.1038/Ncomms6152  0.289
2016 Hao Y, Pierce E, Roe D, Morita M, McIntosh JA, Agarwal V, Cheatham TE, Schmidt EW, Nair SK. Molecular basis for the broad substrate selectivity of a peptide prenyltransferase. Proceedings of the National Academy of Sciences of the United States of America. PMID 27872314 DOI: 10.1073/Pnas.1609869113  0.285
2023 Roe DR, Brooks BR. MPI-parallelization of the grid inhomogeneous solvation theory calculation. Journal of Computational Chemistry. PMID 38071482 DOI: 10.1002/jcc.27278  0.225
2021 Roe DR, Brooks BR. Improving the speed of volumetric density map generation via cubic spline interpolation. Journal of Molecular Graphics & Modelling. 104: 107832. PMID 33444979 DOI: 10.1016/j.jmgm.2021.107832  0.217
2019 Damjanovic A, Chen AY, Rosenberg RL, Roe DR, Wu X, Brooks BR. Protonation state of the selectivity filter of bacterial voltage-gated sodium channels is modulated by ions. Proteins. PMID 31589792 DOI: 10.1002/Prot.25831  0.18
2019 Maginn EJ, Messerly RA, Carlson DJ, Roe DR, Elliott JR. Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0] Living Journal of Computational Molecular Science. 1. DOI: 10.33011/LIVECOMS.1.1.6324  0.161
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  0.12
2022 Roe D, Bäckström Å. Methodological reflections on artistically illustrating ethnographic text from a study of sport pedagogy in youth detention: Ethics, affect, and description. Frontiers in Sports and Active Living. 4: 1021915. PMID 36439624 DOI: 10.3389/fspor.2022.1021915  0.093
2020 Romanella SM, Roe D, Paciorek R, Cappon D, Ruffini G, Menardi A, Rossi A, Rossi S, Santarnecchi E. Sleep, Noninvasive Brain Stimulation, and the Aging Brain: Challenges and Opportunities. Ageing Research Reviews. 61: 101067. PMID 32380212 DOI: 10.1016/J.Arr.2020.101067  0.04
1988 Roe D, Currie J. British Cryogenics Council Symposium Safe Storage and Handling of Cryogenic Liquids Cryogenics. 28: 799. DOI: 10.1016/0011-2275(88)90173-7  0.026
2024 Murray C, Coyle B, Morgan H, Marder I, Woods D, Haughey T, Maycock M, Genovesi F, Meek R, Parker A, Smith A, Kay C, Brink G, Rovers H, Haudenhuyse R, ... Roe D, et al. International consensus statement on the design, delivery and evaluation of sport-based interventions aimed at promoting social, psychological and physical well-being in prison. Bmj Open. 14: e075792. PMID 38296285 DOI: 10.1136/bmjopen-2023-075792  0.019
2022 Tener D, Lusky-Weisrose E, Roe D, Mor R, Sigad LI, Shaharabani M, Yahia-Zetawy Y, Qwekiss-Halabi S, Rozenfeld-Tzafar N. School principals coping with child sexual abuse in their schools. Child Abuse & Neglect. 129: 105656. PMID 35561442 DOI: 10.1016/j.chiabu.2022.105656  0.018
2019 Damjanovic A, Chen AY, Rosenberg RL, Roe D, Brooks BR. Constant pH Study of a Sodium Channel Biophysical Journal. 116: 387a. DOI: 10.1016/J.Bpj.2018.11.2098  0.017
2024 Sigad LI, Gosen NB, Golan L, Lusky-Weisrose E, Shaibe J, Tener D, Moshon-Cohen TE, Roe D. 'A kindergarten teacher must have 100 eyes and 100 ears!': Kindergarten teachers' experiences coping with child sexual abuse and problematic sexual behavior. Child Abuse & Neglect. 151: 106713. PMID 38447239 DOI: 10.1016/j.chiabu.2024.106713  0.01
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