Publications

Filter Year

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
Conformational dynamics and multi-modal interaction of Paxillin with the Focal Adhesion Targeting Domain.
Bhattacharya S, He Y, Chen Y, Mohanty A, Grishaev A, Kulkarni P, Salgia R, Orban J. 2025. Conformational dynamics and multi-modal interaction of Paxillin with the Focal Adhesion Targeting Domain. bioRxiv : the preprint server for biology : . DOI: 10.1101/2025.01.01.630265
Recognition of Self and Viral Ligands by NK Cell Receptors.
Mariuzza RA, Singh P, Karade SS, Shahid S, Sharma VK. 2025. Recognition of Self and Viral Ligands by NK Cell Receptors. Immunological reviews 329(1): e13435. DOI: 10.1111/imr.13435
Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.
Yu W, Weber DJ, MacKerell AD. 2024. Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation. Journal of chemical information and modeling : . DOI: 10.1021/acs.jcim.4c01814
Rapid Removal of IgG1 Carryover on Protease Column Using Protease-Safe Wash Solutions Delivered with LC Pump for HDX-MS Systems.
Kumar S, Anderson KW. 2024. Rapid Removal of IgG1 Carryover on Protease Column Using Protease-Safe Wash Solutions Delivered with LC Pump for HDX-MS Systems. Journal of the American Society for Mass Spectrometry : . DOI: 10.1021/jasms.4c00411
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