Publications

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.
Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ, Weng Z, Pierce BG, Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ, Weng Z, Pierce BG. 2021. An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure (London, England : 1993) 29(6): 606-621.e5. DOI: 10.1016/j.str.2021.01.005
Anti-CfaE nanobodies provide broad cross-protection against major pathogenic enterotoxigenic Escherichia coli strains, with implications for vaccine design.
Amcheslavsky A, Wallace AL, Ejemel M, Li Q, McMahon CT, Stoppato M, Giuntini S, Schiller ZA, Pondish JR, Toomey JR, et al. 2021. Anti-CfaE nanobodies provide broad cross-protection against major pathogenic enterotoxigenic Escherichia coli strains, with implications for vaccine design. Scientific reports 11(1): 2751. DOI: 10.1038/s41598-021-81895-0
Application of bacteriophage-derived endolysins to combat streptococcal disease: current state and perspectives.
Linden SB, Alreja AB, Nelson DC, Linden SB, Alreja AB, Nelson DC. 2021. Application of bacteriophage-derived endolysins to combat streptococcal disease: current state and perspectives. Current opinion in biotechnology 68: 213-220. DOI: 10.1016/j.copbio.2021.01.012
Next generation polyphosphazene immunoadjuvant: Synthesis, self-assembly and in vivo potency with human papillomavirus VLPs-based vaccine.
Marin A, Chowdhury A, Valencia SM, Zacharia A, Kirnbauer R, Roden RBS, Pinto LA, Shoemaker RH, Marshall JD, Andrianov AK, Marin A, Chowdhury A, Valencia SM, Zacharia A, Kirnbauer R, Roden RBS, Pinto LA, Shoemaker RH, Marshall JD, Andrianov AK. 2021. Next generation polyphosphazene immunoadjuvant: Synthesis, self-assembly and in vivo potency with human papillomavirus VLPs-based vaccine. Nanomedicine : nanotechnology, biology, and medicine 33: 102359. DOI: 10.1016/j.nano.2021.102359
Specificity of Molecular Fragments Binding to S100B versus S100A1 as Identified by NMR and Site Identification by Ligand Competitive Saturation (SILCS).
Young BD, Yu W, Rodríguez DJV, Varney KM, MacKerell AD, Weber DJ, Young BD, Yu W, Rodríguez DJV, Varney KM, MacKerell AD, Weber DJ. 2021. Specificity of Molecular Fragments Binding to S100B versus S100A1 as Identified by NMR and Site Identification by Ligand Competitive Saturation (SILCS). Molecules (Basel, Switzerland) 26(2): . DOI: 10.3390/molecules26020381
Discovery of beta-lactamase CMY-10 inhibitors for combination therapy against multi-drug resistant Enterobacteriaceae.
Parvaiz N, Ahmad F, Yu W, MacKerell AD, Azam SS, Parvaiz N, Ahmad F, Yu W, MacKerell AD, Azam SS. 2021. Discovery of beta-lactamase CMY-10 inhibitors for combination therapy against multi-drug resistant Enterobacteriaceae. PloS one 16(1): e0244967. DOI: 10.1371/journal.pone.0244967
Design of a native-like secreted form of the hepatitis C virus E1E2 heterodimer.
Guest JD, Wang R, Elkholy KH, Chagas A, Chao KL, Cleveland TE, Kim YC, Keck ZY, Marin A, Yunus AS, et al. 2021. Design of a native-like secreted form of the hepatitis C virus E1E2 heterodimer. Proceedings of the National Academy of Sciences of the United States of America 118(3): . DOI: 10.1073/pnas.2015149118
Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion.
Borkotoky S, Dey D, Banerjee M, Borkotoky S, Dey D, Banerjee M. 2021. Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion. Journal of chemical information and modeling 61(1): 423-431. DOI: 10.1021/acs.jcim.0c01231
Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components.
Telu KH, Marupaka R, Andriamaharavo NR, Simón-Manso Y, Liang Y, Mirokhin YA, Bukhari TH, Preston RJ, Kashi L, Kelman Z, et al. 2021. Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components. Biotechnology and bioengineering 118(4): 1491-1510. DOI: 10.1002/bit.27661
Small molecules inhibitors of the heterogeneous ribonuclear protein A18 (hnRNP A18): a regulator of protein translation and an immune checkpoint.
Solano-Gonzalez E, Coburn KM, Yu W, Wilson GM, Nurmemmedov E, Kesari S, Chang ET, MacKerell AD, Weber DJ, Carrier F, Solano-Gonzalez E, Coburn KM, Yu W, Wilson GM, Nurmemmedov E, Kesari S, Chang ET, MacKerell AD, Weber DJ, Carrier F. 2021. Small molecules inhibitors of the heterogeneous ribonuclear protein A18 (hnRNP A18): a regulator of protein translation and an immune checkpoint. Nucleic acids research 49(3): 1235-1246. DOI: 10.1093/nar/gkaa1254
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides.
Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z, Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z. 2020. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinformatics (Oxford, England) : . DOI: 10.1093/bioinformatics/btaa1050
Structural Characterization and Modeling of a Respiratory Syncytial Virus Fusion Glycoprotein Nanoparticle Vaccine in Solution.
Krueger S, Curtis JE, Scott DR, Grishaev A, Glenn G, Smith G, Ellingsworth L, Borisov O, Maynard EL, Krueger S, Curtis JE, Scott DR, Grishaev A, Glenn G, Smith G, Ellingsworth L, Borisov O, Maynard EL. 2021. Structural Characterization and Modeling of a Respiratory Syncytial Virus Fusion Glycoprotein Nanoparticle Vaccine in Solution. Molecular pharmaceutics 18(1): 359-376. DOI: 10.1021/acs.molpharmaceut.0c00986
Polyphosphazenes enable durable, hemocompatible, highly efficient antibacterial coatings.
Albright V, Penarete-Acosta D, Stack M, Zheng J, Marin A, Hlushko H, Wang H, Jayaraman A, Andrianov AK, Sukhishvili SA, Albright V, Penarete-Acosta D, Stack M, Zheng J, Marin A, Hlushko H, Wang H, Jayaraman A, Andrianov AK, Sukhishvili SA. 2021. Polyphosphazenes enable durable, hemocompatible, highly efficient antibacterial coatings. Biomaterials 268: 120586. DOI: 10.1016/j.biomaterials.2020.120586
Sand Fly (Phlebotomus papatasi) Embryo Microinjection for CRISPR/Cas9 Mutagenesis.
Louradour I, Ghosh K, Inbar E, Sacks DL, Aluvihare C, Harrell RA, Louradour I, Ghosh K, Inbar E, Sacks DL, Aluvihare C, Harrell RA. 2020. Sand Fly (Phlebotomus papatasi) Embryo Microinjection for CRISPR/Cas9 Mutagenesis. Journal of visualized experiments : JoVE (165): . DOI: 10.3791/61924
Polyphosphazene immunoadjuvants: Historical perspective and recent advances.
Andrianov AK, Langer R, Andrianov AK, Langer R. 2021. Polyphosphazene immunoadjuvants: Historical perspective and recent advances. Journal of controlled release : official journal of the Controlled Release Society 329: 299-315. DOI: 10.1016/j.jconrel.2020.12.001
Sequencing and analysis of gerbera daisy leaf transcriptomes reveal disease resistance and susceptibility genes differentially expressed and associated with powdery mildew resistance.
Bhattarai K, Conesa A, Xiao S, Peres NA, Clark DG, Parajuli S, Deng Z, Bhattarai K, Conesa A, Xiao S, Peres NA, Clark DG, Parajuli S, Deng Z. 2020. Sequencing and analysis of gerbera daisy leaf transcriptomes reveal disease resistance and susceptibility genes differentially expressed and associated with powdery mildew resistance. BMC plant biology 20(1): 539. DOI: 10.1186/s12870-020-02742-4
Crystal Structure of a Bivalent Antibody Fab Fragment.
Shahid S, Gao M, Travis Gallagher D, Pozharski E, Brinson RG, Keck ZY, Foung SKH, Fuerst TR, Mariuzza RA, Shahid S, Gao M, Travis Gallagher D, Pozharski E, Brinson RG, Keck ZY, Foung SKH, Fuerst TR, Mariuzza RA. 2021. Crystal Structure of a Bivalent Antibody Fab Fragment. Journal of molecular biology 433(2): 166714. DOI: 10.1016/j.jmb.2020.11.013
Prospects for Clinical Development of Stat5 Inhibitor IST5-002: High Transcriptomic Specificity in Prostate Cancer and Low Toxicity In Vivo.
Maranto C, Udhane V, Jia J, Verma R, Müller-Newen G, LaViolette PS, Pereckas M, Sabharwal L, Terhune S, Pattabiraman N, et al. 2020. Prospects for Clinical Development of Stat5 Inhibitor IST5-002: High Transcriptomic Specificity in Prostate Cancer and Low Toxicity In Vivo. Cancers 12(11): . DOI: 10.3390/cancers12113412
The SKI complex is a broad-spectrum, host-directed antiviral drug target for coronaviruses, influenza, and filoviruses.
Weston S, Baracco L, Keller C, Matthews K, McGrath ME, Logue J, Liang J, Dyall J, Holbrook MR, Hensley LE, et al. 2020. The SKI complex is a broad-spectrum, host-directed antiviral drug target for coronaviruses, influenza, and filoviruses. Proceedings of the National Academy of Sciences of the United States of America 117(48): 30687-30698. DOI: 10.1073/pnas.2012939117
Quantitative Proteomic Analysis of Biogenesis-Based Classification for Extracellular Vesicles.
Zhang L, Parot J, Hackley VA, Turko IV, Zhang L, Parot J, Hackley VA, Turko IV. 2020. Quantitative Proteomic Analysis of Biogenesis-Based Classification for Extracellular Vesicles. Proteomes 8(4): . DOI: 10.3390/proteomes8040033