IBBR Publications

Found 74 results
Filters: Keyword is Molecular Dynamics Simulation  [Clear All Filters]
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.
Savelyev A, Mackerell AD. Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields. J Phys Chem B. 2015 ;119(12):4428-40.
Chen W, Shi C, Mackerell AD, Shen J. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields. J Phys Chem B. 2015 ;119(25):7902-10.
Yang M, Mackerell AD. Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM). J Chem Theory Comput. 2015 ;11(2):788-99.
Lopes PEM, Guvench O, Mackerell AD. Current status of protein force fields for molecular dynamics simulations. Methods Mol Biol. 2015 ;1215:47-71.
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.
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.
Yang M, Huang J, Mackerell AD. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension. J Chem Theory Comput. 2015 ;11(6):2855-67.
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.
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.
Jo S, Wu EL, Stuhlsatz D, Klauda JB, Mackerell AD, Widmalm G, Im W. Lipopolysaccharide membrane building and simulation. Methods Mol Biol. 2015 ;1273:391-406.
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.
Mallajosyula SS, Jo S, Im W, Mackerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods Mol Biol. 2015 ;1273:407-29.
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.
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.
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.
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.
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.