IBBR Publications

Found 260 results
Filters: Keyword is Protein Binding  [Clear All Filters]
2017
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.
2016
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.
Chen Y, Clarke OB, Kim J, Stowe S, Kim Y-K, Assur Z, Cavalier M, Godoy-Ruiz R, von Alpen DC, Manzini C, et al. Structure of the STRA6 receptor for retinol uptake. Science. 2016 ;353(6302).
2015
Venditti V, Schwieters CD, Grishaev A, G Clore M. Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering. Proc Natl Acad Sci U S A. 2015 ;112(37):11565-70.
Wu EL, Qi Y, Park S, Mallajosyula SS, Mackerell AD, Klauda JB, Im W. Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophys J. 2015 ;109(10):2090-100.
Domene C, Jorgensen C, Vanommeslaeghe K, Schofield CJ, Mackerell AD. Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor. J Chem Theory Comput. 2015 ;11(8):3946-54.
Brusgard JL, Choe M, Chumsri S, Renoud K, Mackerell AD, Sudol M, Passaniti A. RUNX2 and TAZ-dependent signaling pathways regulate soluble E-Cadherin levels and tumorsphere formation in breast cancer cells. Oncotarget. 2015 ;6(29):28132-50.
Faller CE, E Raman P, Mackerell AD, Guvench O. Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design. Methods Mol Biol. 2015 ;1289:75-87.
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.
2014
Haidar JN, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z. Backbone flexibility of CDR3 and immune recognition of antigens. J Mol Biol. 2014 ;426(7):1583-99.
Kern NR, Lee HSun, Wu EL, Park S, Vanommeslaeghe K, Mackerell AD, Klauda JB, Jo S, Im W. Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. Biophys J. 2014 ;107(8):1885-95.
Li T, Yang D, Zhong S, Thomas JM, Xue F, Liu J, Kong L, Voulalas P, Hassan HE, Park J-S, et al. Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models. Hum Mol Genet. 2014 ;23(23):6212-22.
Li Z, Huang RY-C, Yopp DC, Hileman TH, Santangelo TJ, Hurwitz J, Hudgens JW, Kelman Z. A novel mechanism for regulating the activity of proliferating cell nuclear antigen by a small protein. Nucleic Acids Res. 2014 ;42(9):5776-89.
Ofek GA, Zirkle B, Yang Y, Zhu Z, McKee K, Zhang B, Chuang G-Y, Georgiev IS, O'Dell S, Doria-Rose N, et al. Structural basis for HIV-1 neutralization by 2F5-like antibodies m66 and m66.6. J Virol. 2014 ;88(5):2426-41.
2013
S Hasan S, Rizvi A, Naseem I. Calcitriol-induced DNA damage: toward a molecular mechanism of selective cell death. IUBMB Life. 2013 ;65(9):787-92.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JPGLM, Trellet M, Bonvin AMJJ, Cui M, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 2013 ;81(11):1980-7.
Pierce BG, Weng Z. A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes. Protein Sci. 2013 ;22(1):35-46.
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.
E Raman P, Yu W, Lakkaraju SK, Mackerell AD. Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. J Chem Inf Model. 2013 ;53(12):3384-98.
Aduri R, Briggs KT, Gorelick RJ, Marino JP. Molecular determinants of HIV-1 NCp7 chaperone activity in maturation of the HIV-1 dimerization initiation site. Nucleic Acids Res. 2013 ;41(4):2565-80.
Hong X, Ma MZ, Gildersleeve JC, Chowdhury S, Barchi JJ, Mariuzza RA, Murphy MB, Mao L, Pancer Z. Sugar-binding proteins from fish: selection of high affinity "lambodies" that recognize biomedically relevant glycans. ACS Chem Biol. 2013 ;8(1):152-60.
Healy JR, Bezawada P, Shim J, Jones JW, Kane MA, Mackerell AD, Coop A, Matsumoto RR. Synthesis, modeling, and pharmacological evaluation of UMB 425, a mixed μ agonist/δ antagonist opioid analgesic with reduced tolerance liabilities. ACS Chem Neurosci. 2013 ;4(9):1256-66.
S Hasan S, Yamashita E, Cramer WA. Transmembrane signaling and assembly of the cytochrome b6f-lipidic charge transfer complex. Biochim Biophys Acta. 2013 ;1827(11-12):1295-308.
Erzurumlu Y, Kose FAydin, Gozen O, Gozuacik D, Toth EA, Ballar P. A unique IBMPFD-related P97/VCP mutation with differential binding pattern and subcellular localization. Int J Biochem Cell Biol. 2013 ;45(4):773-82.
2012
Huang J, Ofek GA, Laub L, Louder MK, Doria-Rose NA, Longo NS, Imamichi H, Bailer RT, Chakrabarti B, Sharma SK, et al. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature. 2012 ;491(7424):406-12.