| High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations AA Chen, AE García Proceedings of the National Academy of Sciences 110 (42), 16820-16825, 2013 | 332 | 2013 |
| Parameters of monovalent ions in the AMBER-99 forcefield: Assessment of inaccuracies and proposed improvements AA Chen, RV Pappu The Journal of Physical Chemistry B 111 (41), 11884-11887, 2007 | 195 | 2007 |
| Quantitative characterization of ion pairing and cluster formation in strong 1: 1 electrolytes AA Chen, RV Pappu The Journal of Physical Chemistry B 111 (23), 6469-6478, 2007 | 155 | 2007 |
| Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates MY Angela, PM Gasper, L Cheng, LB Lai, S Kaur, V Gopalan, AA Chen, ... Molecular Cell 81 (4), 870-883. e10, 2021 | 82 | 2021 |
| Advances in RNA molecular dynamics: a simulator's guide to RNA force fields S Vangaveti, SV Ranganathan, AA Chen Wiley Interdisciplinary Reviews: RNA, 2016 | 80 | 2016 |
| Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA L Baronti, I Guzzetti, P Ebrahimi, SF Sandoz, E Steiner, J Schlagnitweit, ... Nature 583 (7814), 139-144, 2020 | 79 | 2020 |
| Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop AA Chen, DE Draper, RV Pappu Journal of molecular biology 390 (4), 805-819, 2009 | 79 | 2009 |
| Complex thermodynamic behavior of single-stranded nucleic acid adsorption to graphene surfaces SV Ranganathan, K Halvorsen, CA Myers, NM Robertson, MV Yigit, ... Langmuir 32 (24), 6028-6034, 2016 | 65 | 2016 |
| Simulations of RNA interactions with monovalent ions AA Chen, M Marucho, NA Baker, RV Pappu Methods in enzymology 469, 411-432, 2009 | 56 | 2009 |
| Free-energy landscape of a hyperstable RNA tetraloop JC Miner, AA Chen, AE García Proceedings of the National Academy of Sciences 113 (24), 6665-6670, 2016 | 54 | 2016 |
| The Essential Role of Stacking Adenines in a Two-Base-Pair RNA Kissing Complex W Stephenson, PN Asare-Okai, AA Chen, S Keller, R Santiago, ... Journal of the American Chemical Society 135 (15), 5602-5611, 2013 | 47 | 2013 |
| High-throughput single-molecule quantification of individual base stacking energies in nucleic acids J Abraham Punnoose, KJ Thomas, AR Chandrasekaran, J Vilcapoma, ... Nature Communications 14 (1), 631, 2023 | 41 | 2023 |
| Using in-cell SHAPE-Seq and simulations to probe structure–function design principles of RNA transcriptional regulators MK Takahashi, KE Watters, PM Gasper, TR Abbott, PD Carlson, AA Chen, ... RNA 22 (6), 920-933, 2016 | 41 | 2016 |
| Synthesis, base pairing and structure studies of geranylated RNA R Wang, S Vangaveti, SV Ranganathan, M Basanta-Sanchez, ... Nucleic acids research 44 (13), 6036-6045, 2016 | 37 | 2016 |
| Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch L Cheng, EN White, NL Brandt, MY Angela, AA Chen, JB Lucks Nucleic Acids Research, 10.1093/nar/gkac102, 2022 | 36 | 2022 |
| Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations AA Chen, AE García Proceedings of the National Academy of Sciences 109 (24), E1530-E1539, 2012 | 26 | 2012 |
| Synthesis and base pairing studies of geranylated 2-thiothymidine, a natural variant of thymidine R Wang, SV Ranganathan, M Basanta-Sanchez, F Shen, A Chen, ... Chemical Communications 51 (91), 16369-16372, 2015 | 22 | 2015 |
| Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches RJ D’Esposito, CA Myers, AA Chen, S Vangaveti Genes 13 (3), 540, 2022 | 21 | 2022 |
| A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints P Ebrahimi, S Kaur, L Baronti, K Petzold, AA Chen Methods 162, 96-107, 2019 | 21 | 2019 |
| Hybrid DNA/RNA nanostructures with 2′-5′ linkages AR Chandrasekaran, J Mathivanan, P Ebrahimi, J Vilcapoma, AA Chen, ... Nanoscale 12 (42), 21583-21590, 2020 | 15 | 2020 |
Angel E GarciaCenter for Non Linear Studies, Los Alamos National LaboratoryVerified email at lanl.gov
