IBBR Publications

Found 63 results
Filters: Keyword is Water  [Clear All Filters]
2015
Jana M, Mackerell AD. CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides. J Phys Chem B. 2015 ;119(25):7846-59.
Savelyev A, Mackerell AD. Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding. J Chem Theory Comput. 2015 ;11(9):4473-85.
Kasavajhala K, Bikkina S, Patil I, Mackerell AD, U Priyakumar D. Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution. J Phys Chem B. 2015 ;119(9):3755-61.
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.
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.
Mallajosyula SS, Jo S, Im W, Mackerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods Mol Biol. 2015 ;1273:407-29.
Yu W, Lakkaraju SKaushik, E Raman P, Fang L, Mackerell AD. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. J Chem Inf Model. 2015 ;55(2):407-20.
Patel DS, He X, Mackerell AD. Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator. J Phys Chem B. 2015 ;119(3):637-52.
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.
2013
Lin B, He X, Mackerell AD. A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields. J Phys Chem B. 2013 ;117(36):10572-80.
Vaish A, Silin VI, Walker ML, Steffens KL, Krueger S, Yeliseev AA, Gawrisch K, Vanderah DJ. A generalized strategy for immobilizing uniformly oriented membrane proteins at solid interfaces. Chem Commun (Camb). 2013 ;49(26):2685-7.
Lin B, Lopes PEM, Roux B, Mackerell AD. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. J Chem Phys. 2013 ;139(8):084509.
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.
E Raman P, Mackerell AD. Rapid estimation of hydration thermodynamics of macromolecular regions. J Chem Phys. 2013 ;139(5):055105.
Luo Y, Jiang W, Yu H, Mackerell AD, Roux B. Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discuss. 2013 ;160:135-49; discussion 207-24.
Yu W, Lopes PEM, Roux B, Mackerell AD. Six-site polarizable model of water based on the classical Drude oscillator. J Chem Phys. 2013 ;138(3):034508.