IBBR Publications

Found 524 results
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2015
Lemkul JA, Roux B, van der Spoel D, Mackerell AD. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J Comput Chem. 2015 ;36(19):1473-9.
Mistry P, Laird MHW, Schwarz RS, Greene S, Dyson T, Snyder GA, Xiao TSam, Chauhan J, Fletcher S, Toshchakov VY, et al. Inhibition of TLR2 signaling by small molecule inhibitors targeting a pocket within the TLR2 TIR domain. Proc Natl Acad Sci U S A. 2015 ;112(17):5455-60.
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.
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.
Cheung CSF, Anderson KW, Wang M, Turko IV. Natural flanking sequences for peptides included in a quantification concatamer internal standard. Anal Chem. 2015 ;87(2):1097-102.
Mei Y, Wang Y, Kumari P, Shetty ACarl, Clark D, Gable T, Mackerell AD, Ma MZ, Weber DJ, Yang AJ, et al. A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells. Nat Commun. 2015 ;6:7316.
Cheung CSF, Anderson KW, Benitez KYVillator, Soloski MJ, Aucott JN, Phinney KW, Turko IV. Quantification of Borrelia burgdorferi Membrane Proteins in Human Serum: A New Concept for Detection of Bacterial Infection. Anal Chem. 2015 ;87(22):11383-8.
Anderson KW, Chen J, Wang M, Mast N, Pikuleva IA, Turko IV. Quantification of histone deacetylase isoforms in human frontal cortex, human retina, and mouse brain. PLoS One. 2015 ;10(5):e0126592.
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.
Lee JHo, Li F, Grishaev A, Bax A. Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings. J Am Chem Soc. 2015 ;137(4):1432-5.
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.
Samadani R, Zhang J, Brophy A, Oashi T, U Priyakumar D, E Raman P, St John FJ, Jung K-Y, Fletcher S, Pozharski E, et al. Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf. Biochem J. 2015 ;467(3):425-38.
Fletcher S, Yu W, Huang J, Kwasny SM, Chauhan J, Opperman TJ, Mackerell AD, de Leeuw EPH. Structure-activity exploration of a small-molecule Lipid II inhibitor. Drug Des Devel Ther. 2015 ;9:2383-94.
Hinchliff CE, Smith SA, Allman JF, J Burleigh G, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, et al. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc Natl Acad Sci U S A. 2015 ;112(41):12764-9.
2014
Georgiev IS, Rudicell RS, Saunders KO, Shi W, Kirys T, McKee K, O'Dell S, Chuang G-Y, Yang Z-Y, Ofek GA, et al. Antibodies VRC01 and 10E8 neutralize HIV-1 with high breadth and potency even with Ig-framework regions substantially reverted to germline. J Immunol. 2014 ;192(3):1100-6.
Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HSun, Qi Y, Han W, Vanommeslaeghe K, et al. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Adv Protein Chem Struct Biol. 2014 ;96:235-65.
Trastoy B, Lomino JV, Pierce BG, Carter LG, Günther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang L-X, et al. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Proc Natl Acad Sci U S A. 2014 ;111(18):6714-9.
Sadat MA, Moir S, Chun T-W, Lusso P, Kaplan G, Wolfe L, Memoli MJ, He M, Vega H, J Y Kim L, et al. Glycosylation, hypogammaglobulinemia, and resistance to viral infections. N Engl J Med. 2014 ;370(17):1615-25.
Ofek GA, Diskin R. HIV. Expanding the breadth of an HIV-1 vaccine. Science. 2014 ;346(6215):1290-1.
Lahr DJG, Laughinghouse HDail, Oliverio AM, Gao F, Katz LA. How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth. Bioessays. 2014 ;36(10):950-9.
Min W, Angileri F, Luo H, Lauria A, Shanmugasundaram M, Almerico AMaria, Cappello F, de Macario EConway, Lednev IK, Macario AJL, et al. A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model. Sci Rep. 2014 ;4:6688.
Maltsev AS, Grishaev A, Roche J, Zasloff M, Bax A. Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase. J Am Chem Soc. 2014 ;136(10):3752-5.
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.
Oyer JA, Huang X, Zheng Y, Shim J, Ezponda T, Carpenter Z, Allegretta M, Okot-Kotber CI, Patel JP, Melnick A, et al. Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies. Leukemia. 2014 ;28(1):198-201.
Bird GH, Irimia A, Ofek GA, Kwong PD, Wilson IA, Walensky LD. Stapled HIV-1 peptides recapitulate antigenic structures and engage broadly neutralizing antibodies. Nat Struct Mol Biol. 2014 ;21(12):1058-67.