Publications

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Cryo-EM structures of HCV E2 glycoprotein bound to neutralizing and non-neutralizing antibodies determined using bivalent Fabs as fiducial markers.
Shahid S, Karade SS, Hasan SS, Yin R, Jiang L, Liu Y, Felbinger N, Kulakova L, Toth EA, Keck ZY, et al. 2025. Cryo-EM structures of HCV E2 glycoprotein bound to neutralizing and non-neutralizing antibodies determined using bivalent Fabs as fiducial markers. Communications biology 8(1): 825. DOI: 10.1038/s42003-025-08239-w
Evaluation of Alphafold modeling for elucidation of nanobody-peptide epitope interactions.
Sachdev S, Roy S, Saha SJ, Zhao G, Kumariya R, Creemer BA, Yin R, Pierce BG, Bewley CA, Cheloha RW. 2025. Evaluation of Alphafold modeling for elucidation of nanobody-peptide epitope interactions. The Journal of biological chemistry : 110268. DOI: 10.1016/j.jbc.2025.110268
The crystal structure and biochemical analyses of Escherichia coli YqgF illuminate its diverse functions.
Thakur M, Dhyani KM, Galkin A, Krajewski WW, Yavasani S, Demirkan E, Howard A, Herzberg O, Muniyappa K. 2025. The crystal structure and biochemical analyses of Escherichia coli YqgF illuminate its diverse functions. Journal of molecular biology : 169221. DOI: 10.1016/j.jmb.2025.169221
A comprehensive engineering strategy improves potency and manufacturability of a near pan-neutralizing antibody against HIV.
Sajadi MM, Abbasi A, Tehrani ZR, Siska C, Clark R, Chi W, Seaman MS, Mielke D, Wagh K, Liu Q, et al. 2025. A comprehensive engineering strategy improves potency and manufacturability of a near pan-neutralizing antibody against HIV. Structure (London, England : 1993) : . DOI: 10.1016/j.str.2025.04.016
Non-Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans.
Sharif S, Kumar A, MacKerell AD. 2025. Non-Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans. Journal of computational chemistry 46(14): e70136. DOI: 10.1002/jcc.70136
N-Hydroxypipecolic acid and salicylic acid play key roles in autoimmunity induced by loss of the callose synthase PMR4.
Fan B, Li Z, Jannasch AS, Xiao S, Chen Z. 2025. N-Hydroxypipecolic acid and salicylic acid play key roles in autoimmunity induced by loss of the callose synthase PMR4. Plant physiology : . DOI: 10.1093/plphys/kiaf163
Development and Characterization of the NISTCHO Reference Cell Line.
Dahodwala H, Hodzic I, Slesarev A, Cutak B, Kuzin A, Lal R, Liu J, Mahon J, Narasimhan RL, Onuska J, et al. 2025. Development and Characterization of the NISTCHO Reference Cell Line. Biotechnology journal 20(5): e70012. DOI: 10.1002/biot.70012
The Future of Insomnia Research-There's Still Work to Be Done.
Dressle RJ, Spiegelhalder K, Schiel JE, Benz F, Johann A, Feige B, Jernelöv S, Perlis M, Riemann D. 2025. The Future of Insomnia Research-There's Still Work to Be Done. Journal of sleep research : e70091. DOI: 10.1111/jsr.70091
Glycoengineering of the hepatitis C virus E2 glycoprotein leads to improved biochemical properties and enhanced immunogenicity.
Kulakova L, Li KH, Chiang AWT, Schwoerer MP, Schoffelen S, Elkholy K, Chao KL, Shahid S, Kumar B, Murray NB, et al. 2025. Glycoengineering of the hepatitis C virus E2 glycoprotein leads to improved biochemical properties and enhanced immunogenicity. bioRxiv : the preprint server for biology : . DOI: 10.1101/2025.04.02.646860
High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation.
Yu W, Kumar S, Zhao M, Weber DJ, MacKerell AD. 2025. High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.5c00265
Correction: Protein-polyelectrolyte complexation: effects of sterically repulsive groups, macromolecular architecture and hierarchical assembly.
Hlushko R, Marin A, Andrianov AK. 2025. Correction: Protein-polyelectrolyte complexation: effects of sterically repulsive groups, macromolecular architecture and hierarchical assembly. Soft matter : . DOI: 10.1039/d5sm90071a
Spatial and Sequential Topological Analysis of Molecular Dynamics Simulations of IgG1 Fc Domains.
Kleczynski M, Bergonzo C, Kearsley AJ. 2025. Spatial and Sequential Topological Analysis of Molecular Dynamics Simulations of IgG1 Fc Domains. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.5c00161
Recommended nomenclature convention for the NISTCHO cell line and its product monoclonal antibody, cNISTmAb.
Cleveland MH, Karageorgos IL, Marino JP, Tarlov MJ, Yandrofski KS, Zangmeister RA, Kelman Z. 2025. Recommended nomenclature convention for the NISTCHO cell line and its product monoclonal antibody, cNISTmAb. mAbs 17(1): 2490789. DOI: 10.1080/19420862.2025.2490789
Citrus phloem specific transcriptional profiling through the development of a citrus tristeza virus expressed translating ribosome affinity purification system.
Culver JN, Vallar M, Burchard E, Kamens S, Lair S, Qi Y, Collum TD, Dardick C, El-Mohtar CA, Rogers EE. 2025. Citrus phloem specific transcriptional profiling through the development of a citrus tristeza virus expressed translating ribosome affinity purification system. Plant methods 21(1): 49. DOI: 10.1186/s13007-025-01368-7
The need to implement FAIR principles in biomolecular simulations.
Amaro RE, Åqvist J, Bahar I, Battistini F, Bellaiche A, Beltran D, Biggin PC, Bonomi M, Bowman GR, Bryce RA, et al. 2025. The need to implement FAIR principles in biomolecular simulations. Nature methods : . DOI: 10.1038/s41592-025-02635-0