Publications

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Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.
Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. 2016. Critical assessment of methods of protein structure prediction: Progress and new directions in round XI. Proteins 84 Suppl 1: 4-14. DOI: 10.1002/prot.25064
Dual and Opposing Roles of Xanthine Dehydrogenase in Defense-Associated Reactive Oxygen Species Metabolism in Arabidopsis.
Ma X, Wang W, Bittner F, Schmidt N, Berkey R, Zhang L, King H, Zhang Y, Feng J, Wen Y, et al. 2016. Dual and Opposing Roles of Xanthine Dehydrogenase in Defense-Associated Reactive Oxygen Species Metabolism in Arabidopsis. The Plant cell 28(5): 1108-26. DOI: 10.1105/tpc.15.00880
Maturational characteristics of HIV-specific antibodies in viremic individuals.
Meffre E, Louie A, Bannock J, Kim LJ, Ho J, Frear CC, Kardava L, Wang W, Buckner CM, Wang Y, et al. 2022. Maturational characteristics of HIV-specific antibodies in viremic individuals. JCI insight 1(3): .
A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp.
Altieri AS, Ladner JE, Li Z, Robinson H, Sallman ZF, Marino JP, Kelman Z. 2016. A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp. Nucleic acids research 44(13): 6232-41. DOI: 10.1093/nar/gkw351
Maintenance of HIV-Specific Memory B-Cell Responses in Elite Controllers Despite Low Viral Burdens.
Buckner CM, Kardava L, Zhang X, Gittens K, Justement JS, Kovacs C, McDermott AB, Li Y, Sajadi MM, Chun TW, et al. 2016. Maintenance of HIV-Specific Memory B-Cell Responses in Elite Controllers Despite Low Viral Burdens. The Journal of infectious diseases 214(3): 390-8. DOI: 10.1093/infdis/jiw163
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, et al. 2016. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins 84 Suppl 1: 323-48. DOI: 10.1002/prot.25007
Tobacco mosaic virus-directed reprogramming of auxin/indole acetic acid protein transcriptional responses enhances virus phloem loading.
Collum TD, Padmanabhan MS, Hsieh YC, Culver JN. 2016. Tobacco mosaic virus-directed reprogramming of auxin/indole acetic acid protein transcriptional responses enhances virus phloem loading. Proceedings of the National Academy of Sciences of the United States of America 113(19): E2740-9. DOI: 10.1073/pnas.1524390113
Biodegradable Polyphosphazene Based Peptide-Polymer Hybrids.
Linhardt A, König M, Schöfberger W, Brüggemann O, Andrianov AK, Teasdale I. 2016. Biodegradable Polyphosphazene Based Peptide-Polymer Hybrids. Polymers 8(4): . DOI: 10.3390/polym8040161
Computational Modeling of T Cell Receptor Complexes.
Riley TP, Singh NK, Pierce BG, Weng Z, Baker BM. 2016. Computational Modeling of T Cell Receptor Complexes. Methods in molecular biology (Clifton, N.J.) 1414: 319-40. DOI: 10.1007/978-1-4939-3569-7_19
Computational Reprogramming of T Cell Antigen Receptor Binding Properties.
Riley TP, Singh NK, Pierce BG, Baker BM, Weng Z. 2016. Computational Reprogramming of T Cell Antigen Receptor Binding Properties. Methods in molecular biology (Clifton, N.J.) 1414: 305-18. DOI: 10.1007/978-1-4939-3569-7_18
Evaluation of microbial qPCR workflows using engineered Saccharomyces cerevisiae.
Da Silva SM, Vang LK, Olson ND, Lund SP, Downey AS, Kelman Z, Salit ML, Lin NJ, Morrow JB. 2016. Evaluation of microbial qPCR workflows using engineered Saccharomyces cerevisiae. Biomolecular detection and quantification 7: 27-33. DOI: 10.1016/j.bdq.2016.01.001
Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor.
Kong L, Ju B, Chen Y, He L, Ren L, Liu J, Hong K, Su B, Wang Z, Ozorowski G, et al. 2016. Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor. Immunity 44(4): 939-50. DOI: 10.1016/j.immuni.2016.03.006
Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors.
Quan DN, Tsao CY, Wu HC, Bentley WE. 2016. Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors. PLoS computational biology 12(4): e1004781. DOI: 10.1371/journal.pcbi.1004781
Mapping of the Allosteric Site in Cholesterol Hydroxylase CYP46A1 for Efavirenz, a Drug That Stimulates Enzyme Activity.
Anderson KW, Mast N, Hudgens JW, Lin JB, Turko IV, Pikuleva IA. 2016. Mapping of the Allosteric Site in Cholesterol Hydroxylase CYP46A1 for Efavirenz, a Drug That Stimulates Enzyme Activity. The Journal of biological chemistry 291(22): 11876-86. DOI: 10.1074/jbc.M116.723577
Optimization of the Solubility of HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based Design.
Kwon YD, Georgiev IS, Ofek G, Zhang B, Asokan M, Bailer RT, Bao A, Caruso W, Chen X, Choe M, et al. 2016. Optimization of the Solubility of HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based Design. Journal of virology 90(13): 5899-5914. DOI: 10.1128/JVI.03246-15