2024

32. A. L. Tse, C. M. Acreman, I. Ricardo-Lax, J. Berrigan, G. Lasso, T. Balogun, F. L. Kearns, L. Casalino, G. L. McClain, A. M. Chandran, C. Lemeunier, R. E. Amaro, C. M. Rice, R. K. Jangra, J. S. McLellan, K. Chandran, E. H. Miller. Epistasis between N-terminal and receptor-binding domains drives cell entry in a bat coronavirus spike. PLOS Path., 2024, 20(11), e1012704. (10.1371/journal.ppat.1012704)

31. F. L. Kearns, M. A Rosenfeld, R. E. Amaro. Breaking Down the Bottlebrush: Atomically-Detailed Structural Dynamics of Mucins. J. Chem. Inf. Model., 2024, 64 (20), 7949-7965. (10.1021/acs.jcim.4c00613)

30. W. Hwang, S. Austin, A. Blondel, E. Boittier, S. Boresch, M. Buck, J. Buckner, A. Caflisch, H.-T. Chang, X. Cheng, Y.-K. Choi, J.-W. Chu, Jhih-Wei, M. Crowley, Q. Cui, A. Damjanovic, Y. Deng, M. Devereux, X. Ding, M. Feig, J. Gao, D. Glowacki, J. Gonzales, M. Hamaneh, E. Harder, R. Hayes, J. Huang, Y. Huang, P. Hudson, W. Im, S. Islam, W. Jiang, M. Jones, S. Käser, F. L. Kearns, N. Kern, J. Klauda, T. Lazaridis, J. Lee, J. Lemkul, X. Liu, Y. Luo, A. MacKerell, D. Major, M. Meuwly, K. Nam, L. Nilsson, V. Ovchinnikov, E. Paci, S. Park, R. Pastor, A. Pittman, C. Post, S. Prasad, J. Pu, Y. Qi, T. Rathinavelan, D. Roe, B. Roux, C. Rowley, J. Shen, A. Simmonett, A. Sodt, K. Töpfer, M. Upadhyay, A. van der Vaart, L. I. Vazquez-Salazar, R. Venable, L. Warrensford, H. L. Woodcock, Y. Wu, C. Brooks, B. Brooks, M. Karplus. CHARMM at 45: Enhancements in accessibility, functionality, and speed. J. Phys. Chem. B, 2024. (10.1021/acs.jpcb.4c04100)

29. J. Li, O. Zhang, Y. Wang, K. Sun, X. Guan, D. Bagni, M. Haghighatlari, F. L. Kearns, C. Parks, R. E. Amaro, T. Head-Gordon. Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. J. Chem. Inf. Model., 2024. (10.1021/acs.jcim.4c00634)

28. A. S. F. Oliveira, F. L. Kearns, M. A. Rosenfeld, L. Casalino, I. Berger, C. Schaffitzel, A. D. Davidson, R. E. Amaro, A. J. Mulholland. Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike. eLife, 2024. (10.7554/eLife.97313.1)

27. X. Nuqui,† L. Casalino,† L. Zhou, M. Shehata, A. Wang, A. L. Tse, A. A. Ojha, F. L. Kearns, M. A. Rosenfeld, E. H. Miller, C. M. Acreman, S.-H. Ahn, K. Chandran, J. S. McLellan, R. E. Amaro. Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens. Nat. Commun., 2024, 15, 7370. †Co-first. (10.1038/s41467-024-50976-9)

2023

26. J. Chongsaritsinsuk,† A. Steigmeyer,† K. E. Mahoney,† M. A. Rosenfeld,† T. M. Lucas, D. Ince, F. L. Kearns, A. Battison, M. A. Hollenhorst, D. J. Shon, V. Attah, C. Kwon, C. R. Bertozzi, M. J. Ferracane, R. E. Amaro, S. A. Malaker. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nat. Commun., 2023, 14, 6169. †Co-first. (10.1038/s41467-023-41756-y)

25. S.-H. Kim,† F. L. Kearns (co-first),† M. Rosenfeld, L. Votapka, L. Casalino, M. Papanikolas, R. E. Amaro, R. Freeman. SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. Cell Rep. Phys. Sci., 2023.†Co-first. (10.1016/j.xcrp.2023.101346)

24. S. A. Moghadasi, E. Heilmann, S. N. Moraes, F. L. Kearns, D. von Laer, R. E. Amaro, R. S. Harris. Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. Sci. Adv., 2023. (10.1126/sciadv.ade8778)

2022

23. C. Oh, T. Nakamura, N. Beutler, X. Zhang, J. Piña-Crespo, M. Talantova, S. Ghatak, D. Trudler, L. N. Carnevale, S. R. McKercher, M. A. Bakowski, J. K. Diedrich, A. J. Roberts, A. K. Woods, V. Chi, A. K. Gupta, M. A. Rosenfeld, F. L. Kearns, L. Casalino, N. Shaabani, H. Liu, I. A. Wilson, R. E. Amaro, D. R. Burton, J. R. Yates III, C. Becker, T. F. Rogers, A. K. Chatterjee, S. A. Lipton. Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection. Nat. Chem. Biol., 2022, 19, 275–283. (10.1038/s41589-022-01149-6)

22. F. L. Kearns, D. R. Sandoval, L. Casalino, T. M. Clausen, M. A. Rosenfeld, C. Spliid, R. E. Amaro, J. Esko. Spike-Heparan Sulfate Interactions in SARS-CoV-2 Infection. Curr. Opin. Struct. Biol., 2022, 76, 102439. (10.1016/j.sbi.2022.102439)

21. A. Schöller, F. L. Kearns, H. Lee Woodcock, S. Boresch. Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations. J. Phys. Chem. B, 2022, 126 (15), 2798-2811.(10.1021/acs.jpcb.2c00696)

20. N. Avalon, J. Nafie, C. De Marco Verissimo, L. C. Warrensford, S. G. Dietrick, A. R. Pittman, Ryan M. Young, F. L. Kearns, T. Smalley, J. M. Binning, J. P. Dalton, M. P. Johnson, H. L. Woodcock, A. L. Allcock, B. J. Baker. Tuaimenal A, a Meroterpene from the Irish Deep-Sea Soft Coral Duva florida, Displays Inhibition of the SARS-CoV-2 3CLpro Enzyme. J. Nat. Prod., 2022, 85 (5), 1315-1323. (10.1021/acs.jnatprod.2c00054)

19. C. Laguionie-Marchais, A. L. Allcock, B. J. Baker, E.-A. Conneely, S. G. Dietrick, F. L. Kearns, K. McKeever, R. M. Young, C. A. Sierra, S. Soldatou, S., H. L. Woodcock, M. P. Johnson. Not Drug-like, but Like Drugs: Cnidaria Natural Products. Mar. Drugs, 2022, 20, 42. (10.3390/md20010042)

18. S. L. Vankayala, L. C. Warrensford, A. R. Pittman, F. L. Kearns, J. D. Larkin, H. L. Woodcock. CIFDock: A novel CHARMM-based flexible receptor–flexible ligand docking protocol. J. Comput. Chem., 2022, 43(2), 84. (10.1002/jcc.26759)

17. A. Dommer,† L. Casalino,† F. L. Kearns (co-first),† M. Rosenfeld, N. Wauer, S.-H. Ahn, J. Russo, S. Oliveira, C. Morris, A. Bogetti, A. Trifan, A. Brace, T. Sztain, A. Clyde, H. Ma, C. Chennubhotla, H. Lee, M. Turilli, S. Khalid, T. Tamayo-Mendoza, M. Welborn, A. Christensen, D. G. A. Smith, Z. Qiao, S. K. Sirumalla, M. O’Connor, F. Manby, A. Anandkumar, D. Hardy, J. Phillips, A. Stern, J. Romero, D. Clark, M. Dorrell, T. Maiden, L. Huang, J. McCalpin, C. Woods, A. Gray, M. Williams, B. Barker, H. Rajapaksha, R. Pitts, T. Gibbs, J. Stone, D. Zuckerman, A. Mulholland, T. Miller III, S. Jha, A. Ramanathan, L. Chong, R. E. Amaro. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. Int. J. High Perform. Comput. Appl., 2022. †Co-first. (10.1177/10943420221128233)

2021

16. S.-H. Kim,† F. L. Kearns (co-first),† M. Rosenfeld,† L. Casalino, M. Papanikolas, C. Simmerling, R. E. Amaro, R. Freeman. GlycoGrip: Cell Surface-inspired Universal Sensor for Beta-Coronaviruses. ACS Central Science, 2021. †Co-first. (10.1021/acscentsci.1c01080)

15. A. Szabadi, R. Elfgen, R. Macchieraldo, F. L. Kearns, H. L. Woodcock, B. Kirchner, C. Schröder. Comparison between ab initio and polarizable molecular dynamics simulations of 1-butyl-3-methylimidazolium tetrafluorob-orate and chloride in water. J. Mol. Liq., 2021, 337, 116521. (10.1016/j.molliq.2021.116521)

14. T. Sztain, S.-H. Ahn, A. T. Bogetti, L. Casalino, J. A. Goldsmith, E. Seitz, R. S. McCool, F. L. Kearns, F. Acosta-Reyes, S. Maji, G. Mashayekhi, J. A. McCammon, A. Ourmazd, J. Frank, J. McLellan, L. T. Chong, R. E. Amaro. A Glycan Gate Controls Opening of the SARS-CoV-2 Spike Protein. Nat. Chem., 2021, 13, 963–968. (10.1038/s41557-021-00758-3)

2020

13. K. Zimmerman, F. L. Kearns, R. Tzekov. Natural Protection of the ocular surface from viral infections – A hypothesis. Med. Hypoth., 2020, 143, 110082. (10.1016/j.mehy.2020.110082)

12. B. C. Knott, E. Erickson, E. Topuzlu, M. D. Allen, J. E. Gado, R. Graham, F. L. Kearns, H. P. Austin, G. Dominick, C. W. Johnson, N. A. Rorrer, C. J. Szostkiewicz, V. Copie, C. M. Payne, H. L. Woodcock, B. S. Donohoe, G. T. Beckham, J. E. McGeehan. Characterization and engineering of a two-enzyme system for plastics depolymerization. Proc. Nat. Acad. Sci. 2020. (10.1073/pnas.2006753117)

11. O. A. Pemberton, R. E. Noor, V. Kumar, R. Sanishvili, M. T. Kemp, F. L. Kearns, H. L. Woodcock, I. Gellis, Y. Chen. Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam. Proc. Nat. Acad. Sci.. 2020. (10.1073/pnas.1922203117)

2019

10. H. Valentine, E. Travis, W. El-Adhami, I. Vernos, L. Mosqueda, E. Wayne, F. L. Kearns, L. Bonefont, S. S. Visweswariah, W. Akande-Sholabi, J. Polka. A giant leap for womankind. Nat. Med., 2019, 25, 704–707. (https://rdcu.be/bUuZL)

9. F. L. Kearns (co-first),† C. Robart,† M. T. Kemp, S. L. Vankayala, B. M. Chapin, E. V. Anslyn, H. Lee Woodcock, J. D. Larkin. Modeling Boronic Acid Based Fluorescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid (DMPBA). J. Chem. Inf. Model., 2019, 59, 2150–2158. †Co-first. (10.1021/acs.jcim.8b00987)

8. F. L. Kearns, L. Warrensford, S. Boresch, H. Lee Woodcock. The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations. Mol., 2019, 24, 681–708. (10.3390/molecules24040681)

2018

7. H. P. Austin,† M. D. Allen,† B. S. Donohoe,† N. A. Rorrer,† F. L. Kearns (co-first),† R. Silveira, B. C. Pollard, G. Dominick, R. Duman, K. El-Omari, V. Mykhaylyk, A. Wagner, W. E. Michener, A. Amore, M. S. Skaf, M. F. Crowley, A. W. Thorne, C. W. Johnson, H. Lee Woodcock, J. E. McGeehan, G. T. Beckham. Characterization and engineering of a plastic-degrading aromatic polyesterase. Proc. Nat. Acad. Sci., 2018, 115 E4350–E4357. †Co-first. Note: Altmetric score: 2092, 2018 Altmetric Top 100. (10.1073/pnas.1718804115)

2017

6. F. L. Kearns, P. S. Hudson, H. Lee Woodcock, S. Boresch. Computing converged free energy differences between levels of theory via non-equilibrium work. J. Comput. Chem., 2017; 38, 1376–1388. (10.1002/jcc.24706)

5. S. L. Vankayala,† F. L. Kearns (co-first),† B. J. Baker, J. D. Larkin, H. Lee Woodcock. Elucidating a chemical defense mechanism of Antarctic sponges: A computational study. J. Mol. Graph. Model., 2017; 71, 104–115. †Co-first. (10.1016/j.jmgm.2016.11.004)

2016

4. F. L Kearns, P. S. Hudson, S. Boresch, H. L. Woodcock. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis. Methods Enzymol., 2016; 577, 75–104 (10.1016/bs.mie.2016.05.053)

3. A. S. Mhashilkar, S. L. Vankayala, C. Liu, F. L. Kearns, P. Mehrotra, G. Tzertzinis, S. R. Palli, H. L. Woodcock, T. R. Unnasch. Identification of ecdysone hormone receptor agonists as a therapeutic approach for treating filarial infections. PLoS Neg. Trop. Dis., 2016, 10(6), e0004772. (10.1371/journal.pntd.0004772)

2. G. A. Hunter, S. L. Vankayala, M. E. Gillam, F. L. Kearns, H. L. Woodcock, G. C. Ferreira. The conserved active site histidine-glutamate pair of ferrochelatase coordinately catalyzes porphyrin metalation. J. Porphyr. Phthalocya., 2016, 20, 556–569. (10.1142/S1088424616500395)

2015

1. P. S. Hudson, J. K. White, F. L. Kearns, M. Hodoscek, S. Boresch, H. L. Woodcock. Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes. Biochim. Biophys. Acta, 2015; 1850(5), 944–953. (10.1016/j.bbagen.2014.09.016)