IBBR Publications

Found 80 results
Filters: Keyword is Ligands  [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.
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.
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.
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.
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.
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.