| POVME 2.0: an enhanced tool for determining pocket shape and volume characteristics JD Durrant, L Votapka, J Sørensen, RE Amaro Journal of chemical theory and computation 10 (11), 5047-5056, 2014 | 248 | 2014 |
| Weighted implementation of suboptimal paths (WISP): an optimized algorithm and tool for dynamical network analysis AT Van Wart, J Durrant, L Votapka, RE Amaro Journal of chemical theory and computation 10 (2), 511-517, 2014 | 191 | 2014 |
| Mechanism of 150-cavity formation in influenza neuraminidase RE Amaro, RV Swift, L Votapka, WW Li, RC Walker, RM Bush Nature communications 2 (1), 388, 2011 | 152 | 2011 |
| SEEKR: simulation enabled estimation of kinetic rates, a computational tool to estimate molecular kinetics and its application to trypsin–benzamidine binding LW Votapka, BR Jagger, AL Heyneman, RE Amaro The Journal of Physical Chemistry B 121 (15), 3597-3606, 2017 | 107 | 2017 |
| Multiscale estimation of binding kinetics using Brownian dynamics, molecular dynamics and milestoning LW Votapka, RE Amaro PLoS computational biology 11 (10), e1004381, 2015 | 77 | 2015 |
| Two relations to estimate membrane permeability using milestoning LW Votapka, CT Lee, RE Amaro The Journal of Physical Chemistry B 120 (33), 8606-8616, 2016 | 45 | 2016 |
| SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx SH Kim, FL Kearns, MA Rosenfeld, L Votapka, L Casalino, M Papanikolas, ... Cell Reports Physical Science 4 (4), 2023 | 29 | 2023 |
| Bridging scales through multiscale modeling: a case study on protein kinase A BW Boras, SP Hirakis, LW Votapka, RD Malmstrom, RE Amaro, ... Frontiers in physiology 6, 250, 2015 | 28 | 2015 |
| SEEKR2: Versatile multiscale milestoning utilizing the OpenMM molecular dynamics engine LW Votapka, AM Stokely, AA Ojha, RE Amaro Journal of chemical information and modeling 62 (13), 3253-3262, 2022 | 27 | 2022 |
| A computational assay that explores the hemagglutinin/neuraminidase functional balance reveals the neuraminidase secondary site as a novel anti-influenza target RE Amaro, PU Ieong, G Huber, A Dommer, AC Steven, RM Bush, ... ACS central science 4 (11), 1570-1577, 2018 | 27 | 2018 |
| Multistructural hot spot characterization with FTProd L Votapka, RE Amaro Bioinformatics 29 (3), 393-394, 2013 | 19 | 2013 |
| Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations AA Ojha, A Srivastava, LW Votapka, RE Amaro Journal of Chemical Information and Modeling 63 (8), 2469-2482, 2023 | 16 | 2023 |
| Gaussian accelerated molecular dynamics in OpenMM MM Copeland, HN Do, L Votapka, K Joshi, J Wang, RE Amaro, Y Miao The Journal of Physical Chemistry B 126 (31), 5810-5820, 2022 | 14 | 2022 |
| Brownian dynamics simulations of biomolecular diffusional association processes A Muñiz‐Chicharro, LW Votapka, RE Amaro, RC Wade Wiley Interdisciplinary Reviews: Computational Molecular Science 13 (3), e1649, 2023 | 12 | 2023 |
| Positively bound: remapping of increased positive charge drives SARS-CoV-2 spike evolution to optimize its binding to cell surface receptors SH Kim, FL Kearns, MA Rosenfeld, L Votapka, L Casalino, M Papanikolas, ... American Chemical Society (ACS), 2022 | 8 | 2022 |
| QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations AA Ojha, LW Votapka, RE Amaro Chemical Science 14 (45), 13159-13175, 2023 | 7 | 2023 |
| DelEnsembleElec: Computing ensemble-averaged electrostatics using DelPhi LW Votapka, L Czapla, M Zhenirovskyy, RE Amaro Communications in Computational Physics 13 (1), 256-268, 2013 | 7 | 2013 |
| Variable ligand-and receptor-binding hot spots in key strains of influenza neuraminidase L Votapka, Ö Demir, RV Swift, RC Walker, RE Amaro Journal of Molecular and Genetic Medicine: an International Journal of …, 2012 | 3 | 2012 |
| SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Multiscale Approach for the Calculation of Protein-Ligand Association and Dissociation Kinetics BR Jagger, LW Votapka, RE Amaro Biophysical Journal 114 (3), 42a, 2018 | 2 | 2018 |
| Advances and Challenges in Milestoning Simulations for Drug–Target Kinetics AA Ojha, LW Votapka, RE Amaro Journal of Chemical Theory and Computation 20 (22), 9759-9769, 2024 | 1 | 2024 |
Rommie E. AmaroDistinguished Professorship in Theoretical and Computational Chemistry, UC San Diego.Verified email at ucsd.edu