Publications

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Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR).
Loughran G, Andreev DE, Terenin IM, Namy O, Mikl M, Yordanova MM, McManus CJ, Firth AE, Atkins JF, Fraser CS, et al. 2025. Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR). Nature structural & molecular biology 32(3): 418-430. DOI: 10.1038/s41594-025-01492-x
Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set.
Croitoru A, Kumar A, Lambry JC, Lee J, Sharif S, Yu W, MacKerell AD, Aleksandrov A. 2025. Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.5c00046
Investigating the Interaction between Excipients and Monoclonal Antibodies PGT121 and N49P9.6-FR-LS: A Comprehensive Analysis.
Li X, Orr AA, Sajadi MM, DeVico AL, Deredge DJ, MacKerell AD, Hoag SW. 2025. Investigating the Interaction between Excipients and Monoclonal Antibodies PGT121 and N49P9.6-FR-LS: A Comprehensive Analysis. Molecular pharmaceutics : . DOI: 10.1021/acs.molpharmaceut.4c00973
Thermal proteome profiling and proteome analysis using high-definition mass spectrometry demonstrate modulation of cholesterol biosynthesis by next-generation galeterone analog VNPP433-3β in castration-resistant prostate cancer.
Thankan RS, Thomas E, Weldemariam MM, Purushottamachar P, Huang W, Kane MA, Zhang Y, Ambulos N, Wang BD, Weber D, et al. 2025. Thermal proteome profiling and proteome analysis using high-definition mass spectrometry demonstrate modulation of cholesterol biosynthesis by next-generation galeterone analog VNPP433-3β in castration-resistant prostate cancer. Molecular oncology : . DOI: 10.1002/1878-0261.70009
RNA Helicase DDX3 Interacts with the Capsid Protein of Hepatitis E Virus and Plays a Vital Role in the Viral Replication.
Lin S, Sallapalli BT, Chang P, He J, Coyaud E, Pierce BG, Zhang YJ. 2025. RNA Helicase DDX3 Interacts with the Capsid Protein of Hepatitis E Virus and Plays a Vital Role in the Viral Replication. Pathogens (Basel, Switzerland) 14(2): . DOI: 10.3390/pathogens14020177
First-in-class mitogen-activated protein kinase (MAPK) p38α: MAPK-activated protein kinase 2 dual signal modulator with anti-inflammatory and endothelial-stabilizing properties.
Tulapurkar ME, Shirey KA, Lugkey K, Luo W, Lal R, Galan A, Mahmoud O, McClean N, Thangaraju K, Cericola D, et al. 2024. First-in-class mitogen-activated protein kinase (MAPK) p38α: MAPK-activated protein kinase 2 dual signal modulator with anti-inflammatory and endothelial-stabilizing properties. The Journal of pharmacology and experimental therapeutics 392(3): 100031. DOI: 10.1124/jpet.124.002281
Harnessing novel cytidine deaminases from the animal kingdom for robust multiplexed base editing in rice.
Contiliani DF, Sretenovic S, Dailey M, Zhou M, Cheng Y, Creste S, Xiao S, Qi Y. 2025. Harnessing novel cytidine deaminases from the animal kingdom for robust multiplexed base editing in rice. Plant biotechnology journal : . DOI: 10.1111/pbi.70000
The Lassa Virus Stable Signal Peptide Undergoes a Conformational Change to Aid Viral Fusion.
Collins SD, Jiang L, Liu Y, Lee J. 2025. The Lassa Virus Stable Signal Peptide Undergoes a Conformational Change to Aid Viral Fusion. Chemistry (Weinheim an der Bergstrasse, Germany) 31(18): e202403608. DOI: 10.1002/chem.202403608
Borrelial phosphomannose isomerase as a cell surface localized protein that retains enzymatic activity and promotes host-pathogen interaction.
Dutta S, Rana VS, Backstedt BT, Shakya AK, Kitsou C, Yas OB, Smith AA, Ronzetti MH, Lipman RM, Araujo-Aris S, et al. 2025. Borrelial phosphomannose isomerase as a cell surface localized protein that retains enzymatic activity and promotes host-pathogen interaction. mBio : e0360924. DOI: 10.1128/mbio.03609-24
3D Printed Spectroelectrochemical Platform for Redox-Based Bioelectronics.
Chen CY, Kim E, Zakaria FR, Chu MJ, Wu B, Payne GF, Bentley WE. 2025. 3D Printed Spectroelectrochemical Platform for Redox-Based Bioelectronics. Small methods : e2401843. DOI: 10.1002/smtd.202401843
On the Biosynthesis of Bioactive Tryptamines in Black Cohosh (Actaea racemosa L.).
Spiering MJ, Parsons JF, Eisenstein E. 2025. On the Biosynthesis of Bioactive Tryptamines in Black Cohosh (<i>Actaea racemosa</i> L.). Plants (Basel, Switzerland) 14(2): . DOI: 10.3390/plants14020292
Virus-Mimicking Polymer Nanocomplexes Co-Assembling HCV E1E2 and Core Proteins with TLR 7/8 Agonist-Synthesis, Characterization, and In Vivo Activity.
Fuerst TR, Marin A, Jeong S, Kulakova L, Hlushko R, Gorga K, Toth EA, Singh NJ, Andrianov AK. 2025. Virus-Mimicking Polymer Nanocomplexes Co-Assembling HCV E1E2 and Core Proteins with TLR 7/8 Agonist-Synthesis, Characterization, and In Vivo Activity. Journal of functional biomaterials 16(1): . DOI: 10.3390/jfb16010034
Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field.
Teng X, Yu W, MacKerell AD. 2025. Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field. The journal of physical chemistry letters : 1016-1023. DOI: 10.1021/acs.jpclett.4c03451
AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.
Gowthaman R, Park M, Yin R, Guest JD, Pierce BG. 2025. AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55. Proteins : . DOI: 10.1002/prot.26801
Structure and dynamics of monoclonal antibody domains determined using spins, scattering, and simulations.
Szalai VA, Bergonzo C, Lyon R, Kelman Z, Schmidt T, Grishaev A. 2025. Structure and dynamics of monoclonal antibody domains determined using spins, scattering, and simulations. ChemMedChem : e202400917. DOI: 10.1002/cmdc.202400917