IBBR Publications

Yu Y, Kramer A, Venable RM, Simmonett AC, Mackerell AD, Klauda JB, Pastor RW, Brooks BR. Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. J Chem Theory Comput. 2021 .

Solano-Gonzalez E, Coburn KM, Yu W, Wilson GM, Nurmemmedov E, Kesari S, Chang ET, Mackerell AD, Weber DJ, Carrier F. Small molecules inhibitors of the heterogeneous ribonuclear protein A18 (hnRNP A18): a regulator of protein translation and an immune checkpoint. Nucleic Acids Res. 2021 .

Young BD, Yu W, Rodríguez DJVera, Varney KM, Mackerell AD, Weber DJ. Specificity of Molecular Fragments Binding to S100B versus S100A1 as Identified by NMR and Site Identification by Ligand Competitive Saturation (SILCS). Molecules. 2021 ;26(2).

Krueger S, Curtis JE, Scott DR, Grishaev A, Glenn G, Smith G, Ellingsworth L, Borisov O, Maynard EL. Structural Characterization and Modeling of a Respiratory Syncytial Virus Fusion Glycoprotein Nanoparticle Vaccine in Solution. Mol Pharm. 2021 ;18(1):359-376.

Mousaei M, Kudaibergenova M, Mackerell AD, Noskov S. Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. J Chem Inf Model. 2020 ;60(12):6489-6501.

Arbogast LW, Delaglio F, Brinson RG, Marino JP. Assessment of the Higher-Order Structure of Formulated Monoclonal Antibody Therapeutics by 2D Methyl Correlated NMR and Principal Component Analysis. Curr Protoc Protein Sci. 2020 ;100(1):e105.

Arbogast LW, Delaglio F, Brinson RG, Marino JP. Assessment of the Higher‐Order Structure of Formulated Monoclonal Antibody Therapeutics by 2D Methyl Correlated NMR and Principal Component Analysis. Current Protocols in Protein Science [Internet]. 2020 ;100(1). Available from: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpps.105

Josey BP, Heinrich F, Silin VI, Lösche M. Association of Model Neurotransmitters with Lipid Bilayer Membranes. Biophys J. 2020 .

Weissman JL, Stoltzfus A, Westra ER, Johnson PLF. Avoidance of Self during CRISPR Immunization. Trends Microbiol. 2020 ;28(7):543-553.

Kognole AA, Aytenfisu AH, Mackerell AD. Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides. J Mol Model. 2020 ;26(6):152.

Brinson RG, Arbogast LW, Marino JP, Delaglio F. Best Practices in Utilization of 2D-NMR Spectral Data as the Input for Chemometric Analysis in Biopharmaceutical Applications. J Chem Inf Model. 2020 .

Daniels J, Doukas PG, Escala MEMartinez, Ringbloom KG, Shih DJH, Yang J, Tegtmeyer K, Park J, Thomas JJ, Selli ME, et al. Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas. Nat Commun. 2020 ;11(1):1806.

Elst NVander, Linden SB, Lavigne R, Meyer E, Briers Y, Nelson DC. Characterization of the Bacteriophage-Derived Endolysins PlySs2 and PlySs9 with In Vitro Lytic Activity against Bovine Mastitis . Antibiotics (Basel). 2020 ;9(9).

Lawrence C, Grishaev A. Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR. RNA. 2020 .

Fu H, Zhao M, Xu J, Tan L, Han J, Li D, Wang M, Xiao S, Ma X, Deng Z. Citron C-05 inhibits both the penetration and colonization of subsp. to achieve resistance to citrus canker disease. Hortic Res. 2020 ;7:58.

VanArsdale E, Hörnström D, Sjöberg G, Järbur I, Pitzer J, Payne GF, van Maris AJA, Bentley WE. A Coculture Based Tyrosine-Tyrosinase Electrochemical Gene Circuit for Connecting Cellular Communication with Electronic Networks. ACS Synth Biol. 2020 .

Elliott KW, Ghasriani H, Wikström M, Giddens JP, Aubin Y, Delaglio F, Marino JP, Arbogast LW. Comparative Analysis of 1D PROFILE and 2D 1H,13C Methyl NMR Methods for Characterization of the Higher Order Structure of IgG1 Monoclonal Antibodies. Analytical Chemstry [Internet]. 2020 ;92(9). Available from: https://pubs.acs.org/doi/abs/10.1021/acs.analchem.9b05385

Elliott KW, Ghasriani H, Wikström M, Giddens JP, Aubin Y, Delaglio F, Marino JP, Arbogast LW. Comparative Analysis of One-Dimensional Protein Fingerprint by Line Shape Enhancement and Two-Dimensional H,C Methyl NMR Methods for Characterization of the Higher Order Structure of IgG1 Monoclonal Antibodies. Anal Chem. 2020 .

Jo S, Xu A, Curtis JE, Somani S, Mackerell AD. Computational Characterization of Antibody-Excipient Interactions for Rational Excipient Selection Using the Site Identification by Ligand Competitive Saturation-Biologics Approach. Mol Pharm. 2020 .

Tyukhtenko S, Ma X, Rajarshi G, Karageorgos I, Anderson KW, Hudgens JW, Guo JJ, Nasr ML, Zvonok N, Vemuri K, et al. Conformational gating, dynamics and allostery in human monoacylglycerol lipase. Sci Rep. 2020 ;10(1):18531.

Gowthaman R, Guest JD, Yin R, Adolf-Bryfogle J, Schief WR, Pierce BG. CoV3D: A database of high resolution coronavirus protein structures. bioRxiv. 2020 .

Gowthaman R, Guest JD, Yin R, Adolf-Bryfogle J, Schief WR, Pierce BG. CoV3D: a database of high resolution coronavirus protein structures. Nucleic Acids Res. 2020 .

Wan D-Y, Guo Y, Cheng Y, Hu Y, Xiao S, Wang Y, Wen Y-Q. CRISPR/Cas9-mediated mutagenesis of results in enhanced resistance to powdery mildew in grapevine (). Hortic Res. 2020 ;7:116.

Chen C-L, S Hasan S, Klose T, Sun Y, Buda G, Sun C, Klimstra WB, Rossmann MG. Cryo-EM structure of eastern equine encephalitis virus in complex with heparan sulfate analogues. Proc Natl Acad Sci U S A. 2020 ;117(16):8890-8899.

Sesterhenn F, Yang C, Bonet J, Cramer JT, Wen X, Wang Y, Chiang C-I, Abriata LA, Kucharska I, Castoro G, et al. De novo protein design enables the precise induction of RSV-neutralizing antibodies. Science. 2020 ;368(6492).