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
Simulations of RNA interactions with monovalent ions
AA Chen, M Marucho, NA Baker, RV Pappu
Methods in enzymology 469, 411-432, 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
Advances in RNA molecular dynamics: a simulator's guide to RNA force fields
S Vangaveti, SV Ranganathan, AA Chen
Wiley Interdisciplinary Reviews: RNA, 2016
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
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
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
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
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
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
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
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
Computationally Reconstructing Cotranscriptional RNA Folding Pathways from Experimental Data Reveals Rearrangement of Non-Native Folding Intermediates
MY Angela, PM Gasper, EJ Strobel, KE Watters, AA Chen, JB Lucks
bioRxiv, 379222, 2018
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
Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR
LM Seebald, CM DeMott, S Ranganathan, PN Asare-Okai, A Glazunova, ...
Journal of Inorganic Biochemistry 170, 202-208, 2017
Nature’s Selection of Geranyl Group as a tRNA Modification: The Effects of Chain Length on Base-Pairing Specificity
P Haruehanroengra, S Vangaveti, SV Ranganathan, R Wang, A Chen, ...
ACS Chemical Biology 12 (6), 1504-1513, 2017
Cu (II)-Based Paramagnetic Probe to Study RNA–Protein Interactions by NMR
LM Seebald, CM DeMott, S Ranganathan, PNA Okai, A Glazunova, ...
American Chemical Society, 2017
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