Publications

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Spatial requirements for ITAM signaling in an intracellular natural killer cell model membrane.
Chong G, MacKerell AD. 2022. Spatial requirements for ITAM signaling in an intracellular natural killer cell model membrane. Biochimica et biophysica acta. General subjects : 130221. DOI: 10.1016/j.bbagen.2022.130221
Preserving the Integrity of Empirical Force Fields.
Orr AA, Sharif S, Wang J, MacKerell AD. 2022. Preserving the Integrity of Empirical Force Fields. Journal of chemical information and modeling : . DOI: 10.1021/acs.jcim.2c00615
SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules.
Kognole AA, Hazel A, MacKerell AD. 2022. SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.2c00381
Altered blood-brain barrier transport of nanotherapeutics in lysosomal storage diseases.
Solomon M, Loeck M, Silva-Abreau M, Moscoso R, Bautista R, Vigo M, Muro S. 2022. Altered blood-brain barrier transport of nanotherapeutics in lysosomal storage diseases. Journal of controlled release : official journal of the Controlled Release Society : . DOI: 10.1016/j.jconrel.2022.07.022
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants.
Yin R, Feng BY, Varshney A, Pierce BG. 2022. Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants. Protein science : a publication of the Protein Society 31(8): e4379. DOI: 10.1002/pro.4379
Immunogenicity of Endolysin PlyC.
Harhala MA, Gembara K, Nelson DC, Miernikiewicz P, Dąbrowska K. 2022. Immunogenicity of Endolysin PlyC. Antibiotics (Basel, Switzerland) 11(7): . DOI: 10.3390/antibiotics11070966
Tuning Design Parameters of ICAM-1-Targeted 3DNA Nanocarriers to Optimize Pulmonary Targeting Depending on Drug Type.
Roki N, Solomon M, Bowers J, Getts L, Getts RC, Muro S. 2022. Tuning Design Parameters of ICAM-1-Targeted 3DNA Nanocarriers to Optimize Pulmonary Targeting Depending on Drug Type. Pharmaceutics 14(7): . DOI: 10.3390/pharmaceutics14071496
Editorial overview: Engineering and design.
Fleishman SJ, Mariuzza RA. 2022. Editorial overview: Engineering and design. Current opinion in structural biology 75: 102437. DOI: 10.1016/j.sbi.2022.102437
Structural Features of Antibody-Peptide Recognition.
Lee JH, Yin R, Ofek G, Pierce BG. 2022. Structural Features of Antibody-Peptide Recognition. Frontiers in immunology 13: 910367. DOI: 10.3389/fimmu.2022.910367
Selective C-Terminal Conjugation of Protease-Derived Native Peptides for Proteomic Measurements.
Xie T, Brady A, Velarde C, Vaccarello DN, Callahan NW, Marino JP, Orski SV. 2022. Selective C-Terminal Conjugation of Protease-Derived Native Peptides for Proteomic Measurements. Langmuir : the ACS journal of surfaces and colloids : . DOI: 10.1021/acs.langmuir.2c00359
Bacterial chemotaxis in static gradients quantified in a biopolymer membrane-integrated microfluidic platform.
Hu P, Ly KL, Pham LPH, Pottash AE, Sheridan K, Wu HC, Tsao CY, Quan D, Bentley WE, Rubloff GW, et al. 2022. Bacterial chemotaxis in static gradients quantified in a biopolymer membrane-integrated microfluidic platform. Lab on a chip : . DOI: 10.1039/d2lc00481j
CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.
Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, et al. 2022. CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. Nature reviews. Chemistry 6(4): 287-295. DOI: 10.1038/s41570-022-00363-z
Early human B cell signatures of the primary antibody response to mRNA vaccination.
Kardava L, Rachmaninoff N, Lau WW, Buckner CM, Trihemasava K, Blazkova J, Lopes de Assis F, Wang W, Zhang X, Wang Y, et al. 2022. Early human B cell signatures of the primary antibody response to mRNA vaccination. Proceedings of the National Academy of Sciences of the United States of America 119(28): e2204607119. DOI: 10.1073/pnas.2204607119
Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.
Sengul MY, MacKerell AD. 2022. Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field. Journal of computational biophysics and chemistry 21(4): 461-471. DOI: 10.1142/s2737416521420060
Network-based redox communication between abiotic interactive materials.
Li J, Zhao Z, Kim E, Rzasa JR, Zong G, Wang LX, Bentley WE, Payne GF. 2022. Network-based redox communication between abiotic interactive materials. iScience 25(7): 104548. DOI: 10.1016/j.isci.2022.104548