Publications

Filter Year

Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.
Bergonzo C, Grishaev A. 2025. Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game. Journal of chemical information and modeling : . DOI: 10.1021/acs.jcim.5c00245
Correction: Maranto et al. Prospects for Clinical Development of Stat5 Inhibitor IST5-002: High Transcriptomic Specificity in Prostate Cancer and Low Toxicity In Vivo. Cancers 2020, 12, 3412.
Maranto C, Udhane V, Jia J, Verma R, Müller-Newen G, LaViolette PS, Pereckas M, Sabharwal L, Terhune S, Pattabiraman N, et al. 2025. Correction: Maranto et al. Prospects for Clinical Development of Stat5 Inhibitor IST5-002: High Transcriptomic Specificity in Prostate Cancer and Low Toxicity In Vivo. <i>Cancers</i> 2020, <i>12</i>, 3412. Cancers 17(6): . DOI: 10.3390/cancers17060932
Potent and Selective Human Constitutive Androstane Receptor Activator DL5055 Facilitates Cyclophosphamide-Based Chemotherapies.
Liang D, Li L, Ai Y, Li Z, Hedrich WD, Sakamuru S, Lynch C, Yu W, Watts-Ouattara I, Heyward S, et al. 2025. Potent and Selective Human Constitutive Androstane Receptor Activator DL5055 Facilitates Cyclophosphamide-Based Chemotherapies. Journal of medicinal chemistry : . DOI: 10.1021/acs.jmedchem.4c02064
Mapping the Distribution and Affinities of Ligand Interaction Sites on Human Serum Albumin.
Orr AA, Uwakweh AO, Li X, Karanji AK, Hoag SW, Deredge DJ, MacKerell AD. 2025. Mapping the Distribution and Affinities of Ligand Interaction Sites on Human Serum Albumin. Biophysical journal : . DOI: 10.1016/j.bpj.2025.03.016
Evolving concepts of the protein universe.
Kulkarni P, Porter L, Chou TF, Chong S, Chiti F, Schafer JW, Mohanty A, Ramisetty S, Onuchic JN, Tuite M, et al. 2025. Evolving concepts of the protein universe. iScience 28(3): 112012. DOI: 10.1016/j.isci.2025.112012
Delivery of protein therapeutics and vaccines using their multivalent complexes with synthetic polyelectrolytes.
Andrianov AK. 2025. Delivery of protein therapeutics and vaccines using their multivalent complexes with synthetic polyelectrolytes. Progress in molecular biology and translational science 212: 235-259. DOI: 10.1016/bs.pmbts.2024.04.005
3D nanoprinting of PDMS microvessels with tailored tortuosity and microporosity via direct laser writing.
Xu X, Qiu Y, Chen CY, Carton M, Campbell PMR, Chowdhury AM, Bandyopadhyay BC, Bentley WE, Smith BR, Sochol RD. 2025. 3D nanoprinting of PDMS microvessels with tailored tortuosity and microporosity <i>via</i> direct laser writing. Lab on a chip : . DOI: 10.1039/d4lc01051e
Unveiling the cold reality of metamorphic proteins.
LiWang A, Orban J. 2025. Unveiling the cold reality of metamorphic proteins. Proceedings of the National Academy of Sciences of the United States of America 122(12): e2422725122. DOI: 10.1073/pnas.2422725122
Sleep Health and White Matter Integrity in the UK Biobank.
Petri R, Holub F, Schiel JE, Feige B, Rutter MK, Tamm S, Riemann D, Kyle SD, Spiegelhalder K. 2025. Sleep Health and White Matter Integrity in the UK Biobank. Journal of sleep research : e70034. DOI: 10.1111/jsr.70034
Genomic characterization of the HER2-enriched intrinsic molecular subtype in primary ER-positive HER2-negative breast cancer.
Hohmann L, Sigurjonsdottir K, Campos AB, Nacer DF, Veerla S, Rosengren F, Reddy PT, Häkkinen J, Nordborg N, Vallon-Christersson J, et al. 2025. Genomic characterization of the HER2-enriched intrinsic molecular subtype in primary ER-positive HER2-negative breast cancer. Nature communications 16(1): 2208. DOI: 10.1038/s41467-025-57419-z
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