Publications

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Ligand-Bound Forced Degradation as a Strategy to Generate Functionally Relevant Analytical Challenge Materials for Assessment of CQAs.
Giddens JP, Schiel JE. 2022. Ligand-Bound Forced Degradation as a Strategy to Generate Functionally Relevant Analytical Challenge Materials for Assessment of CQAs. Frontiers in molecular biosciences 9: 789973. DOI: 10.3389/fmolb.2022.789973
Conformational Heterogeneity of UCAAUC RNA Oligonucleotide from Molecular Dynamics Simulations, SAXS, and NMR experiments.
Bergonzo C, Grishaev AV, Bottaro S. 2022. Conformational Heterogeneity of UCAAUC RNA Oligonucleotide from Molecular Dynamics Simulations, SAXS, and NMR experiments. RNA (New York, N.Y.) : . DOI: 10.1261/rna.078888.121
Identification of Endoplasmic Reticulum α-Glucosidase I from a Thermophilic Fungus as a Platform for Structure-Guided Antiviral Drug Design.
Karade SS, Kolesnikov A, Treston AM, Mariuzza RA. 2022. Identification of Endoplasmic Reticulum α-Glucosidase I from a Thermophilic Fungus as a Platform for Structure-Guided Antiviral Drug Design. Biochemistry : . DOI: 10.1021/acs.biochem.2c00092
Cholecalciferol complexation with hydroxypropyl-β-cyclodextrin (HPBCD) and its molecular dynamics simulation.
Wang F, Yu W, Popescu C, Ibrahim AA, Yu D, Pearson R, MacKerell AD, Hoag SW. 2022. Cholecalciferol complexation with hydroxypropyl-β-cyclodextrin (HPBCD) and its molecular dynamics simulation. Pharmaceutical development and technology : 1-10. DOI: 10.1080/10837450.2022.2064492
Controlled Proteolysis of an Essential Virulence Determinant Dictates Infectivity of Lyme Disease Pathogens.
Thakur M, Bista S, Foor SD, Dutta S, Yang X, Ronzetti M, Rana VS, Kitsou C, Linden SB, Altieri AS, et al. 2022. Controlled Proteolysis of an Essential Virulence Determinant Dictates Infectivity of Lyme Disease Pathogens. Infection and immunity : e0005922. DOI: 10.1128/iai.00059-22
Comparison between Nanoparticle Encapsulation and Surface Loading for Lysosomal Enzyme Replacement Therapy.
Muntimadugu E, Silva-Abreu M, Vives G, Loeck M, Pham V, Del Moral M, Solomon M, Muro S. 2022. Comparison between Nanoparticle Encapsulation and Surface Loading for Lysosomal Enzyme Replacement Therapy. International journal of molecular sciences 23(7): . DOI: 10.3390/ijms23074034
A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies.
Lombard-Banek C, Pohl KI, Kwee EJ, Elliott JT, Schiel JE. 2022. A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies. Journal of proteome research : . DOI: 10.1021/acs.jproteome.1c00887
Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.
Chatterjee P, Sengul MY, Kumar A, MacKerell AD. 2022. Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.2c00115
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