Publications

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Understanding the Molecular Basis for Homodimer Formation of the Pneumococcal Endolysin Cpl-1.
Alreja AB, Linden SB, Lee HR, Chao KL, Herzberg O, Nelson DC. 2023. Understanding the Molecular Basis for Homodimer Formation of the Pneumococcal Endolysin Cpl-1. ACS infectious diseases : . DOI: 10.1021/acsinfecdis.2c00627
Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation.
Yu W, Weber DJ, MacKerell AD. 2023. Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.3c00232
Multiple models for outbreak decision support in the face of uncertainty.
Shea K, Borchering RK, Probert WJM, Howerton E, Bogich TL, Li SL, van Panhuis WG, Viboud C, Aguás R, Belov AA, et al. 2023. Multiple models for outbreak decision support in the face of uncertainty. Proceedings of the National Academy of Sciences of the United States of America 120(18): e2207537120. DOI: 10.1073/pnas.2207537120
GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations.
Zhao M, Kognole AA, Jo S, Tao A, Hazel A, MacKerell AD. 2023. GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations. Journal of computational chemistry : . DOI: 10.1002/jcc.27121
4-Methylumbelliferone-Functionalized Polyphosphazene and Its Assembly into Biocompatible Fluorinated Nanocoatings with Selective Antiproliferative Activity.
Tagad HD, Brito J, Marin A, Buckley C, Wang H, Sun J, Sukhishvili SA, Wang H, Andrianov AK. 2023. 4-Methylumbelliferone-Functionalized Polyphosphazene and Its Assembly into Biocompatible Fluorinated Nanocoatings with Selective Antiproliferative Activity. Biomacromolecules : . DOI: 10.1021/acs.biomac.3c00153
Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.
Yu Y, Venable RM, Thirman J, Chatterjee P, Kumar A, Pastor RW, Roux B, MacKerell AD, Klauda JB. 2023. Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.3c00203
A novel de novo variant in CASK causes a severe neurodevelopmental disorder that masks the phenotype of a novel de novo variant in EEF2.
Rodríguez-García ME, Cotrina-Vinagre FJ, Olson AN, Sánchez-Calvin MT, de Aragón AM, de Las Heras RS, Dinman JD, de Vries BBA, Nabais Sá MJ, Quijada-Fraile P, et al. 2023. A novel de novo variant in CASK causes a severe neurodevelopmental disorder that masks the phenotype of a novel de novo variant in EEF2. Journal of human genetics 68(8): 543-550. DOI: 10.1038/s10038-023-01150-4
Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction.
Orr AA, Tao A, Guvench O, MacKerell AD. 2023. Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction. Molecular pharmaceutics : . DOI: 10.1021/acs.molpharmaceut.3c00064
Mutation bias and the predictability of evolution.
Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. 2023. Mutation bias and the predictability of evolution. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 378(1877): 20220055. DOI: 10.1098/rstb.2022.0055
Monomeric crystal structure of the vaccine carrier protein CRM197 and implications for vaccine development.
Gallagher DT, Oganesyan N, Lees A. 2023. Monomeric crystal structure of the vaccine carrier protein CRM197 and implications for vaccine development. Acta crystallographica. Section F, Structural biology communications : . DOI: 10.1107/S2053230X23002364
Delivery of CRISPR-Cas12a Ribonucleoprotein Complex for Genome Editing in an Embryogenic Citrus Cell Line.
Fang H, Culver JN, Niedz RP, Qi Y. 2023. Delivery of CRISPR-Cas12a Ribonucleoprotein Complex for Genome Editing in an Embryogenic Citrus Cell Line. Methods in molecular biology (Clifton, N.J.) 2653: 153-171. DOI: 10.1007/978-1-0716-3131-7_10
Evaluating targeted COVID-19 vaccination strategies with agent-based modeling.
Hladish TJ, Pillai AN, Pearson CAB, Toh KB, Tamayo A, Stoltzfus A, Longini IM. 2023. Evaluating targeted COVID-19 vaccination strategies with agent-based modeling. medRxiv : the preprint server for health sciences : . DOI: 10.1101/2023.03.09.23285319
Editorial: Improving crop health: Understanding the interaction mechanisms between crops and their pathogens.
Yang Y, Zhang Q, Yu Y, Li G, Xiao S, Ma Z. 2023. Editorial: Improving crop health: Understanding the interaction mechanisms between crops and their pathogens. Frontiers in plant science 14: 1161154. DOI: 10.3389/fpls.2023.1161154
Wheat Pore-forming toxin-like protein confers broad-spectrum resistance to fungal pathogens in Arabidopsis.
Singh L, Sinha A, Gupta M, Xiao S, Hammond R, Rawat N. 2023. Wheat Pore-forming toxin-like protein confers broad-spectrum resistance to fungal pathogens in Arabidopsis. Molecular plant-microbe interactions : MPMI : . DOI: 10.1094/MPMI-12-22-0247-R
Cell-Like Capsules with "Smart" Compartments.
Ahn SH, Borden LK, Bentley WE, Raghavan SR. 2023. Cell-Like Capsules with "Smart" Compartments. Small (Weinheim an der Bergstrasse, Germany) : e2206693. DOI: 10.1002/smll.202206693