IBBR Publications

Yin R, Guest JD, Taherzadeh G, Gowthaman R, Mittra I, Quackenbush J, Pierce BG. Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants. PLoS Comput Biol. 2021 ;17(9):e1009380.

Bester SM, Adipietro KA, Funk VL, Myslinski JM, Keul ND, Cheung J, Wilder PT, Wood ZA, Weber DJ, Height JJ, et al. The structural and biochemical impacts of monomerizing human acetylcholinesterase. Protein Sci. 2019 ;28(6):1106-1114.

S Hasan S, Sun C, Kim AS, Watanabe Y, Chen C-L, Klose T, Buda G, Crispin M, Diamond MS, Klimstra WB, et al. Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization. Cell Rep. 2018 ;25(11):3136-3147.e5.

S Hasan S, Miller A, Sapparapu G, Fernandez E, Klose T, Long F, Fokine A, Porta JC, Jiang W, Diamond MS, et al. A human antibody against Zika virus crosslinks the E protein to prevent infection. Nat Commun. 2017 ;8:14722.

Anderson KW, Mast N, Hudgens JW, Lin JB, Turko IV, Pikuleva IA. Mapping of the Allosteric Site in Cholesterol Hydroxylase CYP46A1 for Efavirenz, a Drug That Stimulates Enzyme Activity. J Biol Chem. 2016 ;291(22):11876-86.

Guo M, Zheng Y, Terell JL, Ad M, Opoku-Temeng C, Bentley WE, Sintim HO. Geminal dihalogen isosteric replacement in hydrated AI-2 affords potent quorum sensing modulators. Chem Commun (Camb). 2015 ;51(13):2617-20.

Lakkaraju SKaushik, Yu W, E Raman P, Hershfeld AV, Fang L, Deshpande DA, Mackerell AD. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. J Chem Inf Model. 2015 ;55(3):700-8.

E Raman P, Mackerell AD. Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability. J Am Chem Soc. 2015 ;137(7):2608-21.

S Hasan S, Cramer WA. Internal lipid architecture of the hetero-oligomeric cytochrome b6f complex. Structure. 2014 ;22(7):1008-15.

Tran K, Poulsen C, Guenaga J, de Val N, Alda Nde Val, Wilson R, Sundling C, Li Y, Stanfield RL, Wilson IA, et al. Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign. Proc Natl Acad Sci U S A. 2014 ;111(7):E738-47.

Wang J, Zhuang J, Iyer S, Lin X-Y, Greven MC, Kim B-H, Moore J, Pierce BG, Dong X, Virgil D, et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 ;41(Database issue):D171-6.

Kishor A, Tandukar B, Ly YV, Toth EA, Suarez Y, Brewer G, Wilson GM. Hsp70 is a novel posttranscriptional regulator of gene expression that binds and stabilizes selected mRNAs containing AU-rich elements. Mol Cell Biol. 2013 ;33(1):71-84.

Nagagarajan S, Xue F, Mackerell AD. Impact of substrate protonation and tautomerization states on interactions with the active site of arginase I. J Chem Inf Model. 2013 ;53(2):452-60.

Foster TJ, Mackerell AD, Guvench O. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J Comput Chem. 2012 ;33(23):1880-91.

Manvilla BA, Maiti A, Begley MC, Toth EA, Drohat AC. Crystal structure of human methyl-binding domain IV glycosylase bound to abasic DNA. J Mol Biol. 2012 ;420(3):164-75.

Bacalocostantis I, Mane VP, Kang MS, Goodley AS, Muro S, Kofinas P. Effect of thiol pendant conjugates on plasmid DNA binding, release, and stability of polymeric delivery vectors. Biomacromolecules. 2012 ;13(5):1331-9.

Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Exploring the DNA-recognition potential of homeodomains. Genome Res. 2012 ;22(10):1889-98.

Sundling C, Li Y, Huynh N, Poulsen C, Wilson R, O'Dell S, Feng Y, Mascola JR, Wyatt RT, Hedestam GBKarlsson. High-resolution definition of vaccine-elicited B cell responses against the HIV primary receptor binding site. Sci Transl Med. 2012 ;4(142):142ra96.

Willis CD, Oashi T, Busby B, Mackerell AD, Bloch RJ. Hydrophobic residues in small ankyrin 1 participate in binding to obscurin. Mol Membr Biol. 2012 ;29(2):36-51.

S Hasan S, Cramer WA. Lipid functions in cytochrome bc complexes: an odd evolutionary transition in a membrane protein structure. Philos Trans R Soc Lond B Biol Sci. 2012 ;367(1608):3406-11.

Yap JL, Cao X, Vanommeslaeghe K, Jung K-Y, Peddaboina C, Wilder PT, Nan A, Mackerell AD, W Smythe R, Fletcher S. Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors. Org Biomol Chem. 2012 ;10(15):2928-33.

Wu X, Wang C, O'Dell S, Li Y, Keele BF, Yang Z, Imamichi H, Doria-Rose N, Hoxie JA, Connors M, et al. Selection pressure on HIV-1 envelope by broadly neutralizing antibodies to the conserved CD4-binding site. J Virol. 2012 ;86(10):5844-56.

Wang J, Zhuang J, Iyer S, Lin XY, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 ;22(9):1798-812.

Yin Y, Li Y, Mariuzza RA. Structural basis for self-recognition by autoimmune T-cell receptors. Immunol Rev. 2012 ;250(1):32-48.

Walsh STR. Structural insights into the common γ-chain family of cytokines and receptors from the interleukin-7 pathway. Immunol Rev. 2012 ;250(1):303-16.