IBBR Publications

Found 258 results
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Banavali NK, Mackerell AD. Characterizing structural transitions using localized free energy landscape analysis. PLoS One. 2009 ;4(5):e5525.
Guvench O, Mackerell AD. Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol. 2009 ;19(1):56-61.
Guvench O, Mackerell AD. Computational fragment-based binding site identification by ligand competitive saturation. PLoS Comput Biol. 2009 ;5(7):e1000435.
Lee H-W, Briggs KT, Marino JP. Dissecting structural transitions in the HIV-1 dimerization initiation site RNA using 2-aminopurine fluorescence. Methods. 2009 ;49(2):118-27.
Joseph KS, Moser AC, Basiaga SBG, Schiel JE, Hage DS. Evaluation of alternatives to warfarin as probes for Sudlow site I of human serum albumin: characterization by high-performance affinity chromatography. J Chromatogr A. 2009 ;1216(16):3492-500.
Charpentier TH, Wilder PT, Liriano MA, Varney KM, Zhong S, Coop A, Pozharski E, Mackerell AD, Toth EA, Weber DJ. Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography. Biochemistry. 2009 ;48(26):6202-12.
Battistel MD, Grishaev A, An SSoo A, Castellino FJ, Llinás M. Solution structure and functional characterization of human plasminogen kringle 5. Biochemistry. 2009 ;48(43):10208-19.
Wright NT, Cannon BR, Wilder PT, Morgan MT, Varney KM, Zimmer DB, Weber DJ. Solution structure of S100A1 bound to the CapZ peptide (TRTK12). J Mol Biol. 2009 ;386(5):1265-77.
Liao W-L, Dodder NG, Mast N, Pikuleva IA, Turko IV. Steroid and protein ligand binding to cytochrome P450 46A1 as assessed by hydrogen-deuterium exchange and mass spectrometry. Biochemistry. 2009 ;48(19):4150-8.
Velikovsky CA, Deng L, Tasumi S, Iyer LM, Kerzic MC, Aravind L, Pancer Z, Mariuzza RA. Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen. Nat Struct Mol Biol. 2009 ;16(7):725-30.
Li Y, Cao C, Jia W, Yu L, Mo M, Wang Q, Huang Y, Lim J-M, Ishihara M, Wells L, et al. Structure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule. EMBO J. 2009 ;28(3):286-97.
Haidar JN, Pierce BG, Yu Y, Tong W, Li M, Weng Z. Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC. Proteins. 2009 ;74(4):948-60.
Dey B, Svehla K, Xu L, Wycuff D, Zhou T, Voss G, Phogat A, Chakrabarti BK, Li Y, Shaw G, et al. Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site. PLoS Pathog. 2009 ;5(5):e1000445.
Sorci L, Pan Y, Eyobo Y, Rodionova I, Huang N, Kurnasov O, Zhong S, Mackerell AD, Zhang H, Osterman AL. Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD. Chem Biol. 2009 ;16(8):849-61.
Costa A, van Duinen G, Medagli B, Chong J, Sakakibara N, Kelman Z, Nair SK, Patwardhan A, Onesti S. Cryo-electron microscopy reveals a novel DNA-binding site on the MCM helicase. EMBO J. 2008 ;27(16):2250-8.
Greenhagen BT, Shi K, Robinson H, Gamage S, Bera AK, Ladner JE, Parsons JF. Crystal structure of the pyocyanin biosynthetic protein PhzS. Biochemistry. 2008 ;47(19):5281-9.
Ruan B, London V, Fisher KE, D Gallagher T, Bryan PN. Engineering substrate preference in subtilisin: structural and kinetic analysis of a specificity mutant. Biochemistry. 2008 ;47(25):6628-36.
Xu Y, Colletier J-P, Weik M, Jiang H, Moult J, Silman I, Sussman JL. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray versus molecular dynamics. Biophys J. 2008 ;95(5):2500-11.
Yu W-M, Guvench O, Mackerell AD, Qu C-K. Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. J Med Chem. 2008 ;51(23):7396-404.
Deng L, Cho S, Malchiodi EL, Kerzic MC, Dam J, Mariuzza RA. Molecular architecture of the major histocompatibility complex class I-binding site of Ly49 natural killer cell receptors. J Biol Chem. 2008 ;283(24):16840-9.
Lewandowski AT, Yi H, Luo X, Payne GF, Ghodssi R, Rubloff GW, Bentley WE. Protein assembly onto patterned microfabricated devices through enzymatic activation of fusion pro-tag. Biotechnol Bioeng. 2008 ;99(3):499-507.
Wiehe K, Peterson MW, Pierce BG, Mintseris J, Weng Z. Protein-protein docking: overview and performance analysis. Methods Mol Biol. 2008 ;413:283-314.
Wright NT, Prosser BL, Varney KM, Zimmer DB, Schneider MF, Weber DJ. S100A1 and calmodulin compete for the same binding site on ryanodine receptor. J Biol Chem. 2008 ;283(39):26676-83.
Prosser BL, Wright NT, Hernández-Ochoa EO, Varney KM, Liu Y, Olojo RO, Zimmer DB, Weber DJ, Schneider MF. S100A1 binds to the calmodulin-binding site of ryanodine receptor and modulates skeletal muscle excitation-contraction coupling. J Biol Chem. 2008 ;283(8):5046-57.
Turner KB, Brinson RG, Yi-Brunozzi HYoung, Rausch JW, Miller JT, Le Grice SFJ, Marino JP, Fabris D. Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands. Nucleic Acids Res. 2008 ;36(8):2799-810.