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Aaron T. Frank, Ph.D. - Publications

Affiliations: 
2011 Chemistry - Ph.D. University of California, Irvine, Irvine, CA 
Area:
Theoretical Chemistry and Biophysics
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31 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
2022 Liu Y, Frank AT. Using Selectively Scaled Molecular Dynamics Simulations to Assess Ligand Poses in RNA Aptamers. Journal of Chemical Theory and Computation. PMID 35926894 DOI: 10.1021/acs.jctc.2c00123  0.332
2022 Moudgal N, Arhin G, Frank AT. Using Unassigned NMR Chemical Shifts to Model RNA Secondary Structure. The Journal of Physical Chemistry. A. 126: 2739-2745. PMID 35470661 DOI: 10.1021/acs.jpca.2c00456  0.381
2021 Zhang K, Frank AT. Probabilistic Modeling of RNA Ensembles Using NMR Chemical Shifts. The Journal of Physical Chemistry. B. PMID 34449236 DOI: 10.1021/acs.jpcb.1c05651  0.43
2021 Xie J, Frank AT. RNA Ensembles from Solvent Accessibility Data: Application to the SAM-I Riboswitch Aptamer Domain. The Journal of Physical Chemistry. B. PMID 33818089 DOI: 10.1021/acs.jpcb.0c11503  0.32
2021 Zhang K, Abdallah K, Ajmera P, Finos K, Looka A, Mekhael J, Frank AT. CS-Annotate: A Tool for Using NMR Chemical Shifts to Annotate RNA Structure. Journal of Chemical Information and Modeling. 61: 1545-1549. PMID 33797909 DOI: 10.1021/acs.jcim.1c00006  0.342
2020 Chhabra S, Xie J, Frank AT. RNAPosers: Machine Learning Classifiers for Ribonucleic Acid-Ligand Poses. The Journal of Physical Chemistry. B. PMID 32427491 DOI: 10.1021/Acs.Jpcb.0C02322  0.354
2020 Xie J, Zhang K, Frank AT. PyShifts: A PyMOL Plugin for Chemical Shift-Based Analysis of Biomolecular Ensembles. Journal of Chemical Information and Modeling. PMID 32011127 DOI: 10.1021/Acs.Jcim.9B01039  0.394
2019 Zhang K, Frank AT. Conditional Prediction of Ribonucleic Acid Secondary Structure Using Chemical Shifts. The Journal of Physical Chemistry. B. PMID 31829591 DOI: 10.1021/Acs.Jpcb.9B09814  0.472
2019 Deb I, Frank AT. Accelerating Rare Dissociative Processes in Biomolecules Using Selectively Scaled MD Simulations. Journal of Chemical Theory and Computation. PMID 31509413 DOI: 10.1021/Acs.Jctc.9B00262  0.322
2018 Zhang K, Frank A. RNA Secondary Structure Prediction Guided by Chemical Shifts Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.3657  0.456
2017 Eschweiler JD, Frank AT, Ruotolo BT. Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment. Journal of the American Society For Mass Spectrometry. PMID 28752478 DOI: 10.1007/S13361-017-1757-1  0.356
2017 Wei S, Brooks CL, Frank AT. A rapid solvent accessible surface area estimator for coarse grained molecular simulations. Journal of Computational Chemistry. PMID 28419507 DOI: 10.1002/Jcc.24709  0.538
2016 Frank AT, Andricioaei I. A Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers' Rate Theory. The Journal of Physical Chemistry. B. PMID 27220565 DOI: 10.1021/Acs.Jpcb.6B02654  0.593
2016 Frank AT. Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA-Ligand Poses? Journal of Chemical Information and Modeling. PMID 26771259 DOI: 10.1021/Acs.Jcim.5B00593  0.454
2015 Frank AT, Zhang Q, Al-Hashimi HM, Andricioaei I. Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophysical Journal. 108: 2876-85. PMID 26083927 DOI: 10.1016/J.Bpj.2015.04.041  0.61
2015 Frank AT, Law SM, Ahlstrom LS, Brooks CL. Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models. Journal of Chemical Theory and Computation. 11: 325-331. PMID 25620895 DOI: 10.1021/Ct5009125  0.712
2014 Frank AT, Law SM, Brooks CL. A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA. The Journal of Physical Chemistry. B. 118: 12168-75. PMID 25255209 DOI: 10.1021/Jp508342X  0.723
2014 Law SM, Frank AT, Brooks CL. PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements. Journal of Computational Chemistry. 35: 1757-61. PMID 24995959 DOI: 10.1002/Jcc.23683  0.686
2013 Frank AT, Bae SH, Stelzer AC. Prediction of RNA 1H and 13C chemical shifts: a structure based approach. The Journal of Physical Chemistry. B. 117: 13497-506. PMID 24033307 DOI: 10.1021/Jp407254M  0.472
2013 Miranda MS, Esteves da Silva JC, Castillo A, Frank AT, Greer A, Brown JA, Davis BC, Liebman JF. Amino, Ammonio and Aminioethenes: A Theoretical Study of their Structure and Energetics. Journal of Physical Organic Chemistry. 26: 613-625. PMID 24019594 DOI: 10.1002/Poc.3140  0.52
2013 Frank AT, Horowitz S, Andricioaei I, Al-Hashimi HM. Utility of 1H NMR chemical shifts in determining RNA structure and dynamics. The Journal of Physical Chemistry. B. 117: 2045-52. PMID 23320790 DOI: 10.1021/Jp310863C  0.679
2011 Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM. Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nature Chemical Biology. 7: 553-9. PMID 21706033 DOI: 10.1038/Nchembio.596  0.615
2011 Frank A, Andricioaei I. A comparative study on the ability of two implicit solvent lipid models to predict transmembrane helix tilt angles. The Journal of Membrane Biology. 239: 57-62. PMID 21152910 DOI: 10.1007/S00232-010-9325-7  0.575
2010 Frank AT, Ramsook CB, Otoo HN, Tan C, Soybelman G, Rauceo JM, Gaur NK, Klotz SA, Lipke PN. Structure and function of glycosylated tandem repeats from Candida albicans Als adhesins. Eukaryotic Cell. 9: 405-14. PMID 19820118 DOI: 10.1128/Ec.00235-09  0.322
2010 Ramsook CB, Frank AT, Otoo HN, Tan C, Soybelman G, Rauceo JM, Lipke PN. Tandem Repeats Domain in Candida Albicans Als Adhesins Biophysical Journal. 98: 453a. DOI: 10.1016/J.Bpj.2009.12.2463  0.308
2009 Stelzer AC, Frank AT, Bailor MH, Andricioaei I, Al-Hashimi HM. Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs. Methods (San Diego, Calif.). 49: 167-73. PMID 19699798 DOI: 10.1016/J.Ymeth.2009.08.006  0.655
2009 Frank AT, Stelzer AC, Al-Hashimi HM, Andricioaei I. Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition. Nucleic Acids Research. 37: 3670-9. PMID 19369218 DOI: 10.1093/Nar/Gkp156  0.645
2009 Frank AT, Stelzer A, Andricioaei I, Al-Hashimi H. An RNA Structural Ensemble Derived by Combining MD and Elongated NMR RDCs Provides Evidence for Adaptive Recognition via Conformational Selection Biophysical Journal. 96: 579a. DOI: 10.1016/J.Bpj.2008.12.3026  0.642
2007 Frank AT, Farina NS, Sawwan N, Wauchope OR, Qi M, Brzostowska EM, Chan W, Grasso FW, Haberfield P, Greer A. Natural macrocyclic molecules have a possible limited structural diversity. Molecular Diversity. 11: 115-8. PMID 18027097 DOI: 10.1007/S11030-007-9065-5  0.496
2007 Frank AT, Adenike A, Aebisher D, Greer A, Gao R, Liebman JF. Paradigms and paradoxes: Energetics of the oxidative cleavage of indigo and of other olefins Structural Chemistry. 18: 71-74. DOI: 10.1007/S11224-006-9126-X  0.462
2006 Gandra N, Frank AT, Le Gendre O, Sawwan N, Aebisher D, Liebman JF, Houk KN, Greer A, Gao R. Possible singlet oxygen generation from the photolysis of indigo dyes in methanol, DMSO, water, and ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate Tetrahedron. 62: 10771-10776. DOI: 10.1016/J.Tet.2006.08.095  0.456
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