Publications

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Protein-polyelectrolyte complexation: effects of sterically repulsive groups, macromolecular architecture and hierarchical assembly.
Hlushko R, Marin A, Andrianov AK. 2024. Protein-polyelectrolyte complexation: effects of sterically repulsive groups, macromolecular architecture and hierarchical assembly. Soft matter : . DOI: 10.1039/d4sm01254b
Extracting Orientation and Distance-Dependent Interaction Potentials between Proteins in Solutions Using Small-Angle X-ray/Neutron Scattering.
Liu Y, Hatch HW, Yuan G, Shen VK, Grishaev AV, Panchal J, Blanco M. 2024. Extracting Orientation and Distance-Dependent Interaction Potentials between Proteins in Solutions Using Small-Angle X-ray/Neutron Scattering. The journal of physical chemistry letters : 12401-12407. DOI: 10.1021/acs.jpclett.4c02629
New Cellular Models to Support Preclinical Studies on ICAM-1-Targeted Drug Delivery.
Vigo M, Haro-Martínez E, Ruiz E, Fumadó-Navarro J, Placci M, Muro S. 2024. New Cellular Models to Support Preclinical Studies on ICAM-1-Targeted Drug Delivery. Journal of drug delivery science and technology 101(Pt A): . DOI: 10.1016/j.jddst.2024.106170
Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.
Baral P, Sengul MY, MacKerell AD. 2024. Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme. The Journal of chemical physics 161(22): . DOI: 10.1063/5.0241246
Proline-Selective Electrochemiluminescence Detecting a Single Amino Acid Variation Between A1 and A2 β-Casein Containing Milks.
Kim E, Chen CY, Chu MJ, Hamstra MF, Bentley WE, Payne GF. 2024. Proline-Selective Electrochemiluminescence Detecting a Single Amino Acid Variation Between A1 and A2 β-Casein Containing Milks. Advanced science (Weinheim, Baden-Wurttemberg, Germany) : e2411956. DOI: 10.1002/advs.202411956
Isoform-Specific vs Isoform-Universal Drug Targeting: A New Targeting Paradigm Illustrated by New Anti-ICAM-1 Antibodies.
Vigo M, Placci M, Muro S. 2024. Isoform-Specific vs Isoform-Universal Drug Targeting: A New Targeting Paradigm Illustrated by New Anti-ICAM-1 Antibodies. Journal of drug targeting : 1-19. DOI: 10.1080/1061186X.2024.2438884
Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities.
Kumar A, Goel H, Yu W, Zhao M, MacKerell AD. 2024. Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.4c01165
Isolation of phytoconstituents from an extract of Murraya paniculata with cytotoxicity and antioxidant activities and in silico evaluation of their potential to bind to aldose reductase (AKR1B1).
Shanta AP, Fatema-Tuz-Zohora , Mahtarin R, MacKerell AD, Ahsan M. 2024. Isolation of phytoconstituents from an extract of <i>Murraya paniculata</i> with cytotoxicity and antioxidant activities and <i>in silico</i> evaluation of their potential to bind to aldose reductase (AKR1B1). Journal of biomolecular structure & dynamics : 1-15. DOI: 10.1080/07391102.2024.2435623
Detecting features of antibody structure through their mediator-accessible redox activities.
Motabar D, Kim E, Li J, Zhao Z, Mouchahoir T, Gallagher DT, Schiel JE, Garige M, Sourbier C, Payne GF, et al. 2024. Detecting features of antibody structure through their mediator-accessible redox activities. Nature chemical biology : . DOI: 10.1038/s41589-024-01778-z
Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.
Nan Y, Baral P, Orr AA, Michel HM, Lemkul JA, MacKerell AD. 2024. Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems. The journal of physical chemistry. B : . DOI: 10.1021/acs.jpcb.4c06354
Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens.
Wu D, Yin R, Chen G, Ribeiro-Filho HV, Cheung M, Robbins PF, Mariuzza RA, Pierce BG. 2024. Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens. Science advances 10(47): eadq6150. DOI: 10.1126/sciadv.adq6150
Toripalimab Plus Chemotherapy as a First-Line Therapy for Extensive-Stage Small Cell Lung Cancer: The Phase 3 EXTENTORCH Randomized Clinical Trial.
Cheng Y, Zhang W, Wu L, Zhou C, Wang D, Xia B, Bi M, Fu X, Li C, Lv D, et al. 2024. Toripalimab Plus Chemotherapy as a First-Line Therapy for Extensive-Stage Small Cell Lung Cancer: The Phase 3 EXTENTORCH Randomized Clinical Trial. JAMA oncology : . DOI: 10.1001/jamaoncol.2024.5019
Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.
Teng X, Yu W, MacKerell AD. 2024. Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.4c00966
Biomimetic Redox Capacitor To Control the Flow of Electrons.
Kim E, Zhao Z, Wu S, Li J, Bentley WE, Payne GF. 2024. Biomimetic Redox Capacitor To Control the Flow of Electrons. ACS applied materials & interfaces : . DOI: 10.1021/acsami.4c13032
modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.
Love O, Galindo-Murillo R, Roe DR, Dans PD, Cheatham Iii TE, Bergonzo C. 2024. modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.4c01164