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Atanu Acharya - Publications

Affiliations: 
2011-2016 Chemistry University of Southern California, Los Angeles, CA, United States 
 2017-2018 Chemistry Yale University, New Haven, CT 
 2019-2022 Physics Georgia Institute of Technology, Atlanta, GA 
Area:
quantum chemistry, molecular dynamics simulations, QM/MM simulations, docking calculations, python, tcl, NAMD, VMD, Gaussian, ORCA, and QChem.
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25 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 Stevens CM, Babii SO, Pandya AN, Li W, Li Y, Mehla J, Scott R, Hegde P, Prathipati PK, Acharya A, Liu J, Gumbart JC, North J, Jackson M, Zgurskaya HI. Proton transfer activity of the reconstituted MmpL3 is modulated by substrate mimics and inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 119: e2113963119. PMID 35858440 DOI: 10.1073/pnas.2113963119  0.504
2022 Yu B, Roy Choudhury M, Yang X, Benoit SL, Womack E, Van Mouwerik Lyles K, Acharya A, Kumar A, Yang C, Pavlova A, Zhu M, Yuan Z, Gumbart JC, Boykin DW, Maier RJ, et al. Restoring and Enhancing the Potency of Existing Antibiotics against Drug-Resistant Gram-Negative Bacteria through the Development of Potent Small-Molecule Adjuvants. Acs Infectious Diseases. PMID 35801980 DOI: 10.1021/acsinfecdis.2c00121  0.469
2022 Dahl PJ, Yi SM, Gu Y, Acharya A, Shipps C, Neu J, O'Brien JP, Morzan UN, Chaudhuri S, Guberman-Pfeffer MJ, Vu D, Yalcin SE, Batista VS, Malvankar NS. A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks. Science Advances. 8: eabm7193. PMID 35544567 DOI: 10.1126/sciadv.abm7193  0.733
2022 Acharya A, Yi D, Pavlova A, Agarwal V, Gumbart JC. Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole. Biochemistry. PMID 35072459 DOI: 10.1021/acs.biochem.1c00741  0.547
2021 Zhan Z, Ryoo D, Balusek C, Acharya A, Rydmark MO, Linke D, Gumbart JC. Inward-facing glycine residues create sharp turns in β-barrel membrane proteins. Biochimica Et Biophysica Acta. Biomembranes. 183662. PMID 34097860 DOI: 10.1016/j.bbamem.2021.183662  0.489
2021 Pavlova A, Zhang Z, Acharya A, Lynch DL, Pang YT, Mou Z, Parks JM, Chipot C, Gumbart JC. Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. The Journal of Physical Chemistry Letters. 5494-5502. PMID 34086459 DOI: 10.1021/acs.jpclett.1c01494  0.511
2021 Acharya A, Lynch DL, Pavlova A, Pang YT, Gumbart JC. ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV. Chemical Communications (Cambridge, England). PMID 34019602 DOI: 10.1039/d1cc02305e  0.478
2021 Yi D, Acharya A, Gumbart JC, Gutekunst WR, Agarwal V. Gatekeeping Ketosynthases Dictate Initiation of Assembly Line Biosynthesis of Pyrrolic Polyketides. Journal of the American Chemical Society. PMID 33989500 DOI: 10.1021/jacs.1c02371  0.49
2020 Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, ... Acharya A, et al. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Chemical Science. 12: 1513-1527. PMID 35356437 DOI: 10.1039/d0sc04942e  0.517
2020 Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler K, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen J, Ellingson SR, Forli S, et al. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. Chemrxiv : the Preprint Server For Chemistry. PMID 33200117 DOI: 10.26434/chemrxiv.12725465.v1  0.5
2020 Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, ... Acharya A, et al. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Biorxiv : the Preprint Server For Biology. PMID 32935106 DOI: 10.1101/2020.09.07.286344  0.517
2020 Yalcin SE, O'Brien JP, Gu Y, Reiss K, Yi SM, Jain R, Srikanth V, Dahl PJ, Huynh W, Vu D, Acharya A, Chaudhuri S, Varga T, Batista VS, Malvankar NS. Electric field stimulates production of highly conductive microbial OmcZ nanowires. Nature Chemical Biology. PMID 32807967 DOI: 10.1038/S41589-020-0623-9  0.707
2020 Acharya A, Stockmann J, Beyer L, Rudack T, Nabers A, Gumbart JC, Gerwert K, Batista VS. The Effect of (-)-Epigallocatechin-3-Gallate on the Amyloid-β Secondary Structure. Biophysical Journal. PMID 32579965 DOI: 10.1016/J.Bpj.2020.05.033  0.636
2020 Acharya A, Stockmann J, Beyer L, Nabers A, Gerwert K, Gumbart JC, Batista VS. The Effect of (-)-Epigallocatechin-3-Gallate on the Aβ Secondary Structure Biophysical Journal. 118: 47a. DOI: 10.1016/J.Bpj.2019.11.437  0.604
2019 East KW, Newton JC, Morzan UN, Narkhede Y, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP. Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. Journal of the American Chemical Society. PMID 31885264 DOI: 10.2210/Pdb6O56/Pdb  0.718
2019 Sen T, Mamontova AV, Titelmayer AV, Shakhov AM, Astafiev AA, Acharya A, Lukyanov KA, Krylov AI, Bogdanov AM. Influence of the First Chromophore-Forming Residue on Photobleaching and Oxidative Photoconversion of EGFP and EYFP. International Journal of Molecular Sciences. 20. PMID 31652505 DOI: 10.3390/Ijms20205229  0.549
2019 Chaudhuri S, Acharya A, Nibbering ETJ, Batista VS. Regioselective Ultrafast Photoinduced Electron Transfer from Naphthols to Halocarbon Solvents. The Journal of Physical Chemistry Letters. PMID 31051077 DOI: 10.1021/Acs.Jpclett.9B00410  0.646
2018 Christensen JA, Phelan BT, Chaudhuri S, Acharya A, Batista VS, Wasielewski MR. Phenothiazine Radical Cation Excited States as Super-oxidants for Energy Demanding Reactions. Journal of the American Chemical Society. PMID 29589754 DOI: 10.1021/Jacs.8B01778  0.603
2018 Acharya A, Chaudhuri S, Batista VS. Can TDDFT Describe Excited Electronic States of Naphthol Photoacids? A Closer Look with EOM-CCSD. Journal of Chemical Theory and Computation. PMID 29298059 DOI: 10.1021/Acs.Jctc.7B01101  0.622
2017 Rudshteyn B, Acharya A, Batista VS. Is the Supporting Information the Venue for Reproducibility and Transparency? The Journal of Physical Chemistry. B. 121: 11425-11426. PMID 29281888 DOI: 10.1021/Acs.Jpcb.7B11664  0.677
2017 Rudshteyn B, Acharya A, Batista VS. Is the Supporting Information the Venue for Reproducibility and Transparency? The Journal of Physical Chemistry. A. 121: 9680-9681. PMID 29281886 DOI: 10.1021/acs.jpca.7b11663  0.665
2016 Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chemical Reviews. PMID 27754659 DOI: 10.1021/Acs.Chemrev.6B00238  0.731
2016 Gurunathan PK, Acharya A, Ghosh D, Kosenkov D, Kaliman I, Shao Y, Krylov AI, Slipchenko LV. The Extension of the Effective Fragment Potential Method to Macromolecules. The Journal of Physical Chemistry. B. PMID 27314461 DOI: 10.1021/Acs.Jpcb.6B04166  0.706
2016 Bogdanov AM, Acharya A, Titelmayer AV, Mamontova AV, Bravaya KB, Kolomeisky AB, Lukyanov KA, Krylov AI. Turning on and off photoinduced electron transfer in fluorescent proteins by π-stacking, halide binding, and Tyr145 mutations. Journal of the American Chemical Society. PMID 26999576 DOI: 10.1021/Jacs.6B00092  0.722
2012 Ghosh D, Acharya A, Tiwari SC, Krylov AI. Toward understanding the redox properties of model chromophores from the green fluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects. The Journal of Physical Chemistry. B. 116: 12398-405. PMID 22978512 DOI: 10.1021/Jp305022T  0.614
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