Publications

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Harnessing computational technologies to facilitate antibody-drug conjugate development.
Croitoru A, Orr AA, MacKerell AD. 2025. Harnessing computational technologies to facilitate antibody-drug conjugate development. Nature chemical biology : . DOI: 10.1038/s41589-025-01950-z
Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.
Kretsch RC, Albrecht R, Andersen ES, Chen HA, Chiu W, Das R, Gezelle JG, Hartmann MD, Höbartner C, Hu Y, et al. 2025. Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers. bioRxiv : the preprint server for biology : . DOI: 10.1101/2025.04.15.649049
Conformational dynamics and multimodal 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 multimodal interaction of Paxillin with the focal adhesion targeting domain. Science advances 11(25): eadt9936. DOI: 10.1126/sciadv.adt9936
Advancing Pharmaceutical Security: Noninvasive Detection of Falsified Vaccines and Drugs Using wNMR.
Taraban MB, Briggs KT, Karki P, Grunin L, Yu YB. 2025. Advancing Pharmaceutical Security: Noninvasive Detection of Falsified Vaccines and Drugs Using wNMR. Pharmaceutical research : . DOI: 10.1007/s11095-025-03880-w
Glycoengineering of the hepatitis C virus E2 glycoprotein improves biochemical properties and enhances immunogenicity.
Kulakova L, Li KH, Chiang AWT, Schwoerer MP, Suzuki S, Schoffelen S, Elkholy KH, Chao KL, Shahid S, Kumar B, et al. 2025. Glycoengineering of the hepatitis C virus E2 glycoprotein improves biochemical properties and enhances immunogenicity. NPJ vaccines 10(1): 121. DOI: 10.1038/s41541-025-01161-6
Pore formation by the CDTb component of the Clostridioides difficile binary toxin is Ca2+-dependent.
Abeyawardhane DL, Sevdalis SE, Adipietro KA, Godoy-Ruiz R, Varney KM, Nawaz IF, Spittel AX, Hunter D, Rustandi RR, Silin VI, et al. 2025. Pore formation by the CDTb component of the Clostridioides difficile binary toxin is Ca2+-dependent. Communications biology 8(1): 901. DOI: 10.1038/s42003-025-08343-x
Enhanced Production of HCV E1E2 Subunit Vaccine Candidates via Protein-Protein Interaction Identification in Glycoengineered CHO cells.
Min Wu MY, Rocamora F, Robinson CM, Shin S, Toth EA, Fuerst TR, Maurya S, Lewis NE. 2025. Enhanced Production of HCV E1E2 Subunit Vaccine Candidates via Protein-Protein Interaction Identification in Glycoengineered CHO cells. bioRxiv : the preprint server for biology : . DOI: 10.1101/2025.05.20.655202
Native-like soluble E1E2 glycoprotein heterodimers on self-assembling protein nanoparticles for hepatitis C virus vaccine design.
He L, Lee YZ, Zhang YN, Newby ML, Janus BM, Gonzalez FG, Ward G, DesRoberts C, Hung SH, Giang E, et al. 2025. Native-like soluble E1E2 glycoprotein heterodimers on self-assembling protein nanoparticles for hepatitis C virus vaccine design. bioRxiv : the preprint server for biology : . DOI: 10.1101/2025.05.16.654559
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