IBBR Publications

Found 43 results
Filters: Keyword is Static Electricity  [Clear All Filters]
2018
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.
2017
Small MC, Aytenfisu AH, Lin F-Y, He X, Mackerell AD. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J Comput Aided Mol Des. 2017 ;31(4):349-363.
2016
Gutiérrez ISoteras, Lin F-Y, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL, Mackerell AD. Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions. Bioorg Med Chem. 2016 ;24(20):4812-4825.
2015
Vanommeslaeghe K, Mackerell AD. CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochim Biophys Acta. 2015 ;1850(5):861-71.
Jana M, Mackerell AD. CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides. J Phys Chem B. 2015 ;119(25):7846-59.
2014
S Hasan S, Zakharov SD, Chauvet A, Stadnytskyi V, Savikhin S, Cramer WA. A map of dielectric heterogeneity in a membrane protein: the hetero-oligomeric cytochrome b6f complex. J Phys Chem B. 2014 ;118(24):6614-25.
2013
Hyland LL, Twomey JD, Vogel S, Hsieh AH, Y Yu B. Enhancing biocompatibility of D-oligopeptide hydrogels by negative charges. Biomacromolecules. 2013 ;14(2):406-12.
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.
Joyner K, Taraban MB, Feng Y, Y Yu B. An interplay between electrostatic and polar interactions in peptide hydrogels. Biopolymers. 2013 ;100(2):174-83.
He X, Lopes PEM, Mackerell AD. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator. Biopolymers. 2013 ;99(10):724-38.
Chowdhary J, Harder E, Lopes PEM, Huang L, Mackerell AD, Roux B. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B. 2013 ;117(31):9142-60.
2012
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.
2011
Jo S, Song KC, Desaire H, Mackerell AD, Im W. Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J Comput Chem. 2011 ;32(14):3135-41.
2010
Walsh STR. A biosensor study indicating that entropy, electrostatics, and receptor glycosylation drive the binding interaction between interleukin-7 and its receptor. Biochemistry. 2010 ;49(40):8766-78.
Mittag T, Marsh J, Grishaev A, Orlicky S, Lin H, Sicheri F, Tyers M, Forman-Kay JD. Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure. 2010 ;18(4):494-506.
2009
Wadington MC, Ladner JE, Stourman NV, Harp JM, Armstrong RN. Analysis of the structure and function of YfcG from Escherichia coli reveals an efficient and unique disulfide bond reductase. Biochemistry. 2009 ;48(28):6559-61.
Harder E, Mackerell AD, Roux B. Many-body polarization effects and the membrane dipole potential. J Am Chem Soc. 2009 ;131(8):2760-1.
Lopes PEM, Lamoureux G, Mackerell AD. Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. J Comput Chem. 2009 ;30(12):1821-38.
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.
2008
Lee S-Y, Lim JSun, Culver JN, Harris MT. Coagulation of tobacco mosaic virus in alcohol-water-LiCl solutions. J Colloid Interface Sci. 2008 ;324(1-2):92-8.
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.
2007
Lopes PEM, Lamoureux G, Roux B, Mackerell AD. Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J Phys Chem B. 2007 ;111(11):2873-85.
Pierce BG, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins. 2007 ;67(4):1078-86.
2005
Vorobyov IV, Anisimov VM, Mackerell AD. Polarizable empirical force field for alkanes based on the classical Drude oscillator model. J Phys Chem B. 2005 ;109(40):18988-99.
2004
Patel S, Mackerell AD, Brooks CL. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem. 2004 ;25(12):1504-14.