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Alan A. Chen, Ph.D. - Publications

Affiliations: 
2009 Washington University, Saint Louis, St. Louis, MO 
Area:
General Biophysics, Physical Chemistry, Biochemistry
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Nowzari ZR, Hale M, Ellis J, Biaesch S, Vangaveti S, Reddy K, Chen AA, Berglund JA. Mutation of two intronic nucleotides alters RNA structure and dynamics inhibiting MBNL1 and RBFOX1 regulated splicing of the Insulin Receptor. Biorxiv : the Preprint Server For Biology. PMID 38260517 DOI: 10.1101/2024.01.08.574689  0.416
2023 Hertz LM, White EN, Kuznedelov K, Cheng L, Yu AM, Kakkaramadam R, Severinov K, Chen A, Lucks JB. The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch. Biorxiv : the Preprint Server For Biology. PMID 38106011 DOI: 10.1101/2023.12.05.570056  0.532
2023 Viegas RG, Sanches MN, Chen AA, Paulovich FV, Garcia AE, Leite VBP. Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop. Journal of Chemical Information and Modeling. PMID 37606640 DOI: 10.1021/acs.jcim.3c00426  0.603
2023 Abraham Punnoose J, Thomas KJ, Chandrasekaran AR, Vilcapoma J, Hayden A, Kilpatrick K, Vangaveti S, Chen A, Banco T, Halvorsen K. High-throughput single-molecule quantification of individual base stacking energies in nucleic acids. Nature Communications. 14: 631. PMID 36746949 DOI: 10.1038/s41467-023-36373-8  0.338
2022 Mathivanan J, Bai Z, Chen A, Sheng J. Design, Synthesis, and Characterization of a Novel 2'-5'-Linked Amikacin-Binding Aptamer: An Experimental and MD Simulation Study. Acs Chemical Biology. 17: 3478-3488. PMID 36453647 DOI: 10.1021/acschembio.2c00653  0.426
2022 Cheng L, White EN, Brandt NL, Yu AM, Chen AA, Lucks JB. Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. Nucleic Acids Research. PMID 35348734 DOI: 10.1093/nar/gkac102  0.453
2022 D'Esposito RJ, Myers CA, Chen AA, Vangaveti S. Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches. Genes. 13. PMID 35328093 DOI: 10.3390/genes13030540  0.529
2021 Yu AM, Gasper PM, Cheng L, Lai LB, Kaur S, Gopalan V, Chen AA, Lucks JB. Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates. Molecular Cell. PMID 33453165 DOI: 10.1016/j.molcel.2020.12.017  0.777
2020 Haruehanroengra P, Vangaveti S, Ranganathan SV, Mao S, Su MD, Chen AA, Sheng J. Terpene Chain Length Affects the Base Pairing Discrimination of -geranyl-2-thiouridine in RNA Duplex. Iscience. 23: 101866. PMID 33319183 DOI: 10.1016/j.isci.2020.101866  0.347
2020 Chandrasekaran AR, Mathivanan J, Ebrahimi P, Vilcapoma J, Chen AA, Halvorsen K, Sheng J. Hybrid DNA/RNA nanostructures with 2'-5' linkages. Nanoscale. PMID 33089274 DOI: 10.1039/d0nr05846g  0.468
2020 Baronti L, Guzzetti I, Ebrahimi P, Friebe Sandoz S, Steiner E, Schlagnitweit J, Fromm B, Silva L, Fontana C, Chen AA, Petzold K. Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA. Nature. PMID 32461691 DOI: 10.1038/S41586-020-2336-3  0.352
2019 Ebrahimi P, Kaur S, Baronti L, Petzold K, Chen AA. A two-dimensional Replica-Exchange Molecular Dynamics method for simulating RNA folding using sparse experimental restraints. Methods (San Diego, Calif.). PMID 31059830 DOI: 10.1016/J.Ymeth.2019.05.001  0.605
2019 Myers CA, D'Esposito RJ, Fabris D, Ranganathan SV, Chen AA. CoSIMS: An Optimized Trajectory Based Collision Simulator for Ion Mobility Spectrometry. The Journal of Physical Chemistry. B. PMID 31042389 DOI: 10.1021/Acs.Jpcb.9B01018  0.327
2018 Mao S, Ranganathan SV, Tsai HC, Haruehanroengra P, Shen F, Valsangkar VA, Han B, Hassan AEA, Chen A, Sheng J. Cyano-modification on Uridine Decrease the Base Pairing Stability and Specificity through Neighbouring Disruption in RNA Duplex. Chembiochem : a European Journal of Chemical Biology. PMID 30294879 DOI: 10.1002/Cbic.201800399  0.564
2017 Haruehanroengra P, Vangaveti S, Ranganathan SV, Wang R, Chen A, Sheng J. Nature's Selection of Geranyl Group as a tRNA Modification: The Effects of Chain Length on Base-Pairing Specificity. Acs Chemical Biology. PMID 28418649 DOI: 10.1021/Acschembio.7B00108  0.354
2017 Seebald LM, DeMott CM, Ranganathan S, Asare Okai PN, Glazunova A, Chen A, Shekhtman A, Royzen M. Cu(II)-Based Paramagnetic Probe to Study RNA-Protein Interactions by NMR. Inorganic Chemistry. PMID 28328212 DOI: 10.1021/Acs.Inorgchem.6B02286  0.472
2017 Seebald LM, DeMott CM, Ranganathan S, Asare-Okai PN, Glazunova A, Chen A, Shekhtman A, Royzen M. Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR. Journal of Inorganic Biochemistry. 170: 202-208. PMID 28260679 DOI: 10.1016/j.jinorgbio.2017.02.024  0.398
2017 Ebrahimi P, Chen A. Simulating the Melting of the Salmonella 4-U RNA Thermometer Using Replica Exchange Molecular Dynamics to Assess Force-Field Accuracy Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.2007  0.494
2016 Vangaveti S, Ranganathan SV, Chen AA. Advances in RNA molecular dynamics: a simulator's guide to RNA force fields. Wiley Interdisciplinary Reviews. Rna. PMID 27704698 DOI: 10.1002/Wrna.1396  0.573
2016 Wang R, Vangaveti S, Ranganathan SV, Basanta-Sanchez M, Haruehanroengra P, Chen A, Sheng J. Synthesis, base pairing and structure studies of geranylated RNA. Nucleic Acids Research. PMID 27307604 DOI: 10.1093/Nar/Gkw544  0.58
2016 Miner JC, Chen AA, García AE. Free-energy landscape of a hyperstable RNA tetraloop. Proceedings of the National Academy of Sciences of the United States of America. PMID 27233937 DOI: 10.1073/Pnas.1603154113  0.703
2016 Takahashi MK, Watters KE, Gasper PM, Abbott TR, Carlson PD, Chen AA, Lucks JB. Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators. Rna (New York, N.Y.). PMID 27103533 DOI: 10.1261/Rna.054916.115  0.768
2016 Huynh LK, Chen A. Designing an Electrochemically Labelled Thrombin DNA Aptamer using Molecular Dynamics Simulations Biophysical Journal. 110: 566a. DOI: 10.1016/J.Bpj.2015.11.3029  0.392
2016 Vangaveti S, Ranganathan S, Sarachan KL, Agris PF, Chen A, Cantara W. Understanding the Effect of Post Transcriptional Modifications in the Anticodon Stem Loop of E.coli tRNA Arginine Biophysical Journal. 110: 235a. DOI: 10.1016/J.Bpj.2015.11.1297  0.42
2015 Wang R, Ranganathan SV, Valsangkar VA, Magliocco SM, Shen F, Chen A, Sheng J. Water-bridged hydrogen bond formation between 5-hydroxylmethylcytosine (5-hmC) and its 3'-neighbouring bases in A- and B-form DNA duplexes. Chemical Communications (Cambridge, England). PMID 26411524 DOI: 10.1039/C5Cc06563A  0.325
2015 Wang R, Ranganathan SV, Basanta-Sanchez M, Shen F, Chen A, Sheng J. Synthesis and base pairing studies of geranylated 2-thiothymidine, a natural variant of thymidine. Chemical Communications (Cambridge, England). PMID 26405057 DOI: 10.1039/C5Cc07479G  0.338
2015 Stephenson W, Colvin A, Chen AA, Li PT. 102 Force and temperature dependent folding of a 2-base-pair RNA kissing complex. Journal of Biomolecular Structure & Dynamics. 33: 65. PMID 26103313 DOI: 10.1080/07391102.2015.1032664  0.521
2015 Chen AA. 87 Recent progress in determining RNA 3D structure and dynamics using all-atom molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics. 33: 57. PMID 26103298 DOI: 10.1080/07391102.2015.1032704  0.484
2015 Garcia AE, Miner J, Chen AA. Reversible Folding of Hyperstable RNA Tetraloops Using Molecular Dynamics Simulations Biophysical Journal. 108: 370a. DOI: 10.1016/J.Bpj.2014.11.2029  0.693
2015 Gasper PM, Chen AA. Sequence Specificity in RNA-Mediated Transcriptional Attenuation Examined by Coarse-Grained MD Simulations Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1314  0.779
2015 Miner JC, Chen AA, García AE. Molecular Simulations Studies of RNA Tetraloop Hyperstability: The Effect of Stem Length on Folding Dynamics Biophysical Journal. 108: 237a. DOI: 10.1016/J.Bpj.2014.11.1313  0.712
2015 Stephenson WT, Colvin A, Chen A, Li PTX. Force and Temperature Dependent Folding of a 2-Base-Pair RNA Kissing Complex Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1299  0.452
2015 Vembanur S, Halvorsen K, Myers C, Chen A, Yigit M. Molecular Modeling and Simulations of DNA at Graphene-Water Interfaces towards Developing Biosensors and Drug Delivery Vehicles Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1279  0.307
2014 Miner JC, Chen AA, Garcia AE. De Novo Folding of RNA Hairpins by Temperature Replica Exchange Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.1642  0.706
2013 Chen AA, García AE. High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 110: 16820-5. PMID 24043821 DOI: 10.1073/Pnas.1309392110  0.614
2013 Stephenson W, Asare-Okai PN, Chen AA, Keller S, Santiago R, Tenenbaum SA, Garcia AE, Fabris D, Li PT. The essential role of stacking adenines in a two-base-pair RNA kissing complex. Journal of the American Chemical Society. 135: 5602-11. PMID 23517345 DOI: 10.1021/Ja310820H  0.701
2013 Stephenson W, Asare-Okai PN, Chen AA, Tenenbaum S, Garcia AE, Fabris D, Li PT. 41 The essential adenosine stacking in a two-base-pair minimal kissing complex Journal of Biomolecular Structure and Dynamics. 31: 25-25. DOI: 10.1080/07391102.2013.786474  0.467
2013 Li PT, Stephenson W, Nii Asare-Okai P, Chen AA, Tenenbaum S, Garcia AE, Fabris D. The Essential Adenosine Stacking in a Two-Base-Pair Minimal Kissing Complex Biophysical Journal. 104: 411a. DOI: 10.1080/07391102.2013.786474  0.62
2012 Chen AA, García AE. Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 109: E1530-9. PMID 22623526 DOI: 10.1073/Pnas.1119552109  0.557
2012 Chen AA, García AE. Mechanism of Enhanced Mechanical Stability of Retroviral Kissing-Loops Elucidated by Non-Equilibrium Molecular Dynamics Simulations Biophysical Journal. 102: 644a-645a. DOI: 10.1016/J.Bpj.2011.11.3508  0.676
2011 Chen AA, Garcia AE. Atomistic Simulations of the Force-Induced Dissociation of Retroviral RNA Kissing-Loops Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3065  0.648
2009 Chen AA, Marucho M, Baker NA, Pappu RV. Simulations of RNA interactions with monovalent ions. Methods in Enzymology. 469: 411-32. PMID 20946801 DOI: 10.1016/S0076-6879(09)69020-0  0.691
2009 Chen AA, Draper DE, Pappu RV. Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. Journal of Molecular Biology. 390: 805-19. PMID 19482035 DOI: 10.1016/J.Jmb.2009.05.071  0.692
2009 Chen AA, Draper DE, Pappu RV. Mechanism Of Monovalent Counterion Specificity In A RNA Kissing Loop Complex Biophysical Journal. 96: 576a. DOI: 10.1016/J.Bpj.2008.12.3008  0.648
2007 Chen AA, Pappu RV. Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements. The Journal of Physical Chemistry. B. 111: 11884-7. PMID 17887792 DOI: 10.1021/Jp0765392  0.523
2007 Chen AA, Pappu RV. Quantitative characterization of ion pairing and cluster formation in strong 1:1 electrolytes. The Journal of Physical Chemistry. B. 111: 6469-78. PMID 17518490 DOI: 10.1021/Jp0708547  0.538
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