Publications
2024
"modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields," O. Love, R. Galindo-Murillo, D. R. Roe, P. D. Dans, T. E. Cheatham III and C. Bergonzo, Journal of Chemical Theory and Computation, 20 (21) pp. 9354-9363 (2024). [DOI] [URL]
"CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed," W. Hwang, S. L. Austin, A. Blondel, E. D. Boittier, S. Boresch, M. Buck, J. Buckner, A. Caflisch, H.-T. Chang, X. Cheng, Y. K. Choi, J.-W. Chu, M. F. Crowley, Q. Cui, A. Damjanovic, Y. Deng, M. Devereux, X. Ding, M. F. Feig, J. Gao, D. R. Glowacki, J. E. I. I. Gonzales, M. B. Hamaneh, E. D. Harder, R. L. Hayes, J. Huang, Y. Huang, P. S. Hudson, W. Im, S. M. Islam, W. Jiang, M. R. Jones, S. Käser, F. L. Kearns, N. R. Kern, J. B. Klauda, T. Lazaridis, J. Lee, J. A. Lemkul, X. Liu, Y. Luo, A. D. J. MacKerell, D. T. Major, M. Meuwly, K. Nam, L. Nilsson, V. Ovchinnikov, E. Paci, S. Park, R. W. Pastor, A. R. Pittman, C. B. Post, S. Prasad, J. Pu, Y. Qi, T. Rathinavelan, D. R. Roe, B. Roux, C. N. Rowley, J. Shen, A. C. Simmonett, A. J. Sodt, K. Töpfer, M. Upadhyay, A. van der Vaart, L. I. Vazquez-Salazar, R. M. Venable, L. C. Warrensford, H. L. Woodcock, Y. Wu, C. L. I. I. I. Brooks, B. R. Brooks and M. Karplus, J. Phys. Chem. B, (2024). [DOI] [URL]
"k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations," L. Chen, D. R. Roe, M. Kochert, C. Simmerling and R. A. Miranda-Quintana, J. Chem. Theory Comput., (2024). [DOI] [URL]
2023
"MPI-parallelization of the grid inhomogeneous solvation theory calculation," D. R. Roe and B. R. Brooks, Journal of Computational Chemistry, (2023). [DOI] [URL]
"AmberTools," D. A. Case, H. M. Aktulga, K. Belfon, D. S. Cerutti, G. A. Cisneros, V. W. D. Cruzeiro, N. Forouzesh, T. J. Giese, A. W. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M. C. Kaymak, E. King, T. Kurtzman, T.-S. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Manathunga, M. R. Machado, H. M. Nguyen, K. A. O’Hearn, A. V. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T. E. III. Cheatham, D. R. Roe, A. Roitberg, C. Simmerling, D. M. York, M. C. Nagan and K. M. J. Merz, J. Chem. Inf. Model., 63 (20) pp. 6183-6191 (2023). [DOI] [URL]
2022
"Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories," D. R. Roe and B. R. Brooks, Protein Science, 31 (12) (2022). [DOI] [URL]
"prepareforleap : An automated tool for fast PDB-to-parameter generation," D. R. Roe and C. Bergonzo, Journal of Computational Chemistry, 43 (13) pp. 930-935 (2022). [DOI] [URL]
2021
"Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory," L. Chen, A. Cruz, D. R. Roe, A. C. Simmonett, L. Wickstrom, N. Deng and T. Kurtzman, J. Chem. Theory Comput., , In Journal of Chemical Theory and Computation. 17 (5) pp. 2714-2724 American Chemical Society. (2021). [DOI] [URL]
"Improving the Speed of Volumetric Density Map Generation via Cubic Spline Interpolation," D. R. Roe and B. R. Brooks, Journal of Molecular Graphics and Modelling, pp. 107832 (2021). [DOI] [URL]
2020
"A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations," D. R. Roe and B. R. Brooks, The Journal of Chemical Physics, 153 (5) pp. 054123 (2020). [DOI] [URL]
2019
"Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]," E. J. Maginn, R. A. Messerly, D. J. Carlson, D. R. Roe and J. R. Elliott, Living Journal of Computational Molecular Science, 1 (1) (2019). [DOI] [URL]
"Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]," A. Grossfield, P. N. Patrone, D. R. Roe, A. J. Schultz, D. Siderius and D. M. Zuckerman, Living Journal of Computational Molecular Science, 1 (1) (2019). [DOI] [URL]
"Polyhedral Compilation Support for C++ Features: A Case Study with CPPTRAJ," A. Roy, D. Roe, M. Hall and T. Cheatham, , In Languages and Compilers for Parallel Computing. pp. 26-35 Springer International Publishing. (2019). [DOI] [URL]
"Direct diabatization and analytic representation of coupled potential energy surfaces and couplings for the reactive quenching of the excited 2Σ+ state of OH by molecular hydrogen," Y. Shu, J. Kryven, A. G. Sampaio de Oliveira-Filho, L. Zhang, G.-L. Song, S. L. Li, R. Meana-Pañeda, B. Fu, J. M. Bowman and D. G. Truhlar, J. Chem. Phys., 151 (10) pp. 104311 (2019). [DOI] [URL]
2018
"Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data," D. R. Roe and T. E. Cheatham, Journal of Computational Chemistry, 39 (25) pp. 2110-2117 (2018). [DOI] [URL]
2017
"Anharmonicity of Coupled Torsions: The Extended Two-Dimensional Torsion Method and Its Use To Assess More Approximate Methods," L. Simón-Carballido, J. L. Bao, T. V. Alves, R. Meana-Pañeda, D. G. Truhlar and A. Fernández-Ramos, Journal of Chemical Theory and Computation, 13 (8) pp. 3478-3492 (2017). [DOI]
"Computational Kinetics by Variational Transition-State Theory with Semiclassical Multidimensional Tunneling: Direct Dynamics Rate Constants for the Abstraction of H from CH3OH by Triplet Oxygen Atoms," R. Meana-Pañeda, X. Xu, H. Ma and D. G. Truhlar, The Journal of Physical Chemistry A, 121 (8) pp. 1693-1707 (2017). [DOI]
"Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA," H. S. Hayatshahi, D. R. Roe, R. Galindo-Murillo, K. B. Hall and T. E. Cheatham, The Journal of Physical Chemistry B, 121 (3) pp. 451-462 (2017). [DOI] [URL]
2016
"A quasiclassical trajectory study of the N2(X1Σ) + O(3P) → NO(X2Π) + N(4S) reaction," W. Lin, R. Meana-Pañeda, Z. Varga and D. G. Truhlar, The Journal of Chemical Physics, 144 (23) pp. 234314 (2016). [DOI] [URL]
"Potential energy surface of triplet N2O2," Z. Varga, R. Meana-Pañeda, G. Song, Y. Paukku and D. G. Truhlar, The Journal of Chemical Physics, 144 (2) pp. 024310 (2016). [DOI] [URL]
"Molecular basis for the broad substrate selectivity of a peptide prenyltransferase," Y. Hao, E. Pierce, D. Roe, M. Morita, J. A. McIntosh, V. Agarwal, T. E. Cheatham, E. W. Schmidt and S. K. Nair, Proceedings of the National Academy of Sciences, 113 (49) pp. 14037-14042 (2016). [DOI] [URL]
"An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors," P. Laurino, Á. Tóth-Petróczy, R. Meana-Pañeda, W. Lin, D. G. Truhlar and D. S. Tawfik, PLOS Biology, 14 (3) pp. 1-23 (2016). [DOI] [URL]