Alan A Chen
Alan A Chen
Associate Professor, Chemistry, SUNY Albany
Verified email at - Homepage
Cited by
Cited by
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
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
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
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
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
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
Advances in RNA molecular dynamics: a simulator's guide to RNA force fields
S Vangaveti, SV Ranganathan, AA Chen
Wiley Interdisciplinary Reviews: RNA, 2016
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
Simulations of RNA interactions with monovalent ions
AA Chen, M Marucho, NA Baker, RV Pappu
Methods in enzymology 469, 411-432, 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
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
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
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
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
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
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
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
CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry
CA Myers, RJ D’Esposito, D Fabris, SV Ranganathan, AA Chen
The Journal of Physical Chemistry B 123 (20), 4347-4357, 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
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
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