IBBR Publications

Found 80 results
Filters: Keyword is Ligands  [Clear All Filters]
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.
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.
2014
Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HSun, Qi Y, Han W, Vanommeslaeghe K, et al. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Adv Protein Chem Struct Biol. 2014 ;96:235-65.
Yu W, Lakkaraju SKaushik, E Raman P, Mackerell AD. Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. J Comput Aided Mol Des. 2014 ;28(5):491-507.
2013
Ha J-H, Eo Y, Grishaev A, Guo M, Smith JAI, Sintim HO, Kim E-H, Cheong H-K, Bentley WE, Ryu K-S. Crystal structures of the LsrR proteins complexed with phospho-AI-2 and two signal-interrupting analogues reveal distinct mechanisms for ligand recognition. J Am Chem Soc. 2013 ;135(41):15526-35.
Huang RY-C, Hudgens JW. Effects of desialylation on human α1-acid glycoprotein-ligand interactions. Biochemistry. 2013 ;52(40):7127-36.
Lakkaraju SKaushik, Xue F, Faden AI, Mackerell AD. Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations. J Chem Inf Model. 2013 ;53(6):1337-49.
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.
Shim J, Coop A, Mackerell AD. Molecular details of the activation of the μ opioid receptor. J Phys Chem B. 2013 ;117(26):7907-17.
2012
Foster TJ, Mackerell AD, Guvench O. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J Comput Chem. 2012 ;33(23):1880-91.
Muro S. Challenges in design and characterization of ligand-targeted drug delivery systems. J Control Release. 2012 ;164(2):125-37.
Chao KL, Tsai I-W, Chen C, Herzberg O. Crystal structure of the Sema-PSI extracellular domain of human RON receptor tyrosine kinase. PLoS One. 2012 ;7(7):e41912.
Sundling C, Li Y, Huynh N, Poulsen C, Wilson R, O'Dell S, Feng Y, Mascola JR, Wyatt RT, Hedestam GBKarlsson. High-resolution definition of vaccine-elicited B cell responses against the HIV primary receptor binding site. Sci Transl Med. 2012 ;4(142):142ra96.
Pettibone JM, Hudgens JW. Predictive gold nanocluster formation controlled by metal-ligand complexes. Small. 2012 ;8(5):715-25.
McElroy CA, Holland PJ, Zhao P, Lim J-M, Wells L, Eisenstein E, Walsh STR. Structural reorganization of the interleukin-7 signaling complex. Proc Natl Acad Sci U S A. 2012 ;109(7):2503-8.
2011
Shim J, Coop A, Mackerell AD. Consensus 3D model of μ-opioid receptor ligand efficacy based on a quantitative Conformationally Sampled Pharmacophore. J Phys Chem B. 2011 ;115(22):7487-96.
Pettibone JM, Hudgens JW. Gold cluster formation with phosphine ligands: etching as a size-selective synthetic pathway for small clusters?. ACS Nano. 2011 ;5(4):2989-3002.
Hudgens JW, Pettibone JM, Senftle TP, Bratton RN. Reaction mechanism governing formation of 1,3-bis(diphenylphosphino)propane-protected gold nanoclusters. Inorg Chem. 2011 ;50(20):10178-89.