Publications

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prepareforleap: An automated tool for fast PDB-to-parameter generation.
Roe DR, Bergonzo C. 2022. prepareforleap: An automated tool for fast PDB-to-parameter generation. Journal of computational chemistry 43(13): 930-935. DOI: 10.1002/jcc.26847
Induction of broadly neutralizing antibodies using a secreted form of the hepatitis C virus E1E2 heterodimer as a vaccine candidate.
Wang R, Suzuki S, Guest JD, Heller B, Almeda M, Andrianov AK, Marin A, Mariuzza RA, Keck ZY, Foung SKH, et al. 2022. Induction of broadly neutralizing antibodies using a secreted form of the hepatitis C virus E1E2 heterodimer as a vaccine candidate. Proceedings of the National Academy of Sciences of the United States of America 119(11): e2112008119. DOI: 10.1073/pnas.2112008119
Structural Fingerprinting of Short Interfering RNA Therapeutics by Solution Nuclear Magnetic Resonance Spectroscopy.
Becette OB, Tran A, Jones JW, Marino JP, Brinson RG. 2022. Structural Fingerprinting of Short Interfering RNA Therapeutics by Solution Nuclear Magnetic Resonance Spectroscopy. Nucleic acid therapeutics : . DOI: 10.1089/nat.2021.0098
Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.
Goel H, Hazel A, Yu W, Jo S, MacKerell AD. 2022. Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design. New journal of chemistry = Nouveau journal de chimie 46(3): 919-932. DOI: 10.1039/d1nj04028f
Highly Efficient Genome Editing in Plant Protoplasts by Ribonucleoprotein Delivery of CRISPR-Cas12a Nucleases.
Zhang Y, Cheng Y, Fang H, Roberts N, Zhang L, Vakulskas CA, Niedz RP, Culver JN, Qi Y. 2022. Highly Efficient Genome Editing in Plant Protoplasts by Ribonucleoprotein Delivery of CRISPR-Cas12a Nucleases. Frontiers in genome editing 4: 780238. DOI: 10.3389/fgeed.2022.780238
Mutation bias shapes the spectrum of adaptive substitutions.
Cano AV, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. 2022. Mutation bias shapes the spectrum of adaptive substitutions. Proceedings of the National Academy of Sciences of the United States of America 119(7): . DOI: 10.1073/pnas.2119720119
Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field.
Kumar A, Pandey P, Chatterjee P, MacKerell AD. 2022. Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.1c01166
Structure of Escherichia coli O157:H7 bacteriophage CBA120 tailspike protein 4 baseplate anchor and tailspike assembly domains (TSP4-N).
Chao KL, Shang X, Greenfield J, Linden SB, Alreja AB, Nelson DC, Herzberg O. 2022. Structure of Escherichia coli O157:H7 bacteriophage CBA120 tailspike protein 4 baseplate anchor and tailspike assembly domains (TSP4-N). Scientific reports 12(1): 2061. DOI: 10.1038/s41598-022-06073-2
An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking.
Dey D, Singh S, Khan S, Martin M, Schnicker NJ, Gakhar L, Pierce BG, Hasan SS. 2022. An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking. Communications biology 5(1): 115. DOI: 10.1038/s42003-022-03063-y
T cell receptors (TCRs) employ diverse strategies to target a p53 cancer neoantigen.
Wu D, Gowathaman R, Pierce BG, Mariuzza RA. 2022. T cell receptors (TCRs) employ diverse strategies to target a p53 cancer neoantigen. The Journal of biological chemistry : 101684. DOI: 10.1016/j.jbc.2022.101684
A Fc-enhanced NTD-binding non-neutralizing antibody delays virus spread and synergizes with a nAb to protect mice from lethal SARS-CoV-2 infection.
Beaudoin-Bussières G, Chen Y, Ullah I, Prévost J, Tolbert WD, Symmes K, Ding S, Benlarbi M, Gong SY, Tauzin A, et al. 2022. A Fc-enhanced NTD-binding non-neutralizing antibody delays virus spread and synergizes with a nAb to protect mice from lethal SARS-CoV-2 infection. Cell reports : 110368. DOI: 10.1016/j.celrep.2022.110368
Electrogenetic Signal Transmission and Propagation in Coculture to Guide Production of a Small Molecule, Tyrosine.
VanArsdale E, Pitzer J, Wang S, Stephens K, Chen CY, Payne GF, Bentley WE. 2022. Electrogenetic Signal Transmission and Propagation in Coculture to Guide Production of a Small Molecule, Tyrosine. ACS synthetic biology : . DOI: 10.1021/acssynbio.1c00522
Electro-assembly of a dynamically adaptive molten fibril state for collagen.
Lei M, Qu X, Wan H, Jin D, Wang S, Zhao Z, Yin M, Payne GF, Liu C. 2022. Electro-assembly of a dynamically adaptive molten fibril state for collagen. Science advances 8(5): eabl7506. DOI: 10.1126/sciadv.abl7506
Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia.
Hiregange DG, Rivalta A, Bose T, Breiner-Goldstein E, Samiya S, Cimicata G, Kulakova L, Zimmerman E, Bashan A, Herzberg O, et al. 2022. Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia. Nucleic acids research : . DOI: 10.1093/nar/gkac046
Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes.
Green AT, Pickard AJ, Li R, MacKerell AD, Bierbach U, Cho SS. 2022. Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes. The journal of physical chemistry. B : . DOI: 10.1021/acs.jpcb.1c08340