IBBR Publications

Found 17 results
Filters: Author is Vanommeslaeghe, Kenno  [Clear All Filters]
2017
Burns LA, Faver JC, Zheng Z, Marshall MS, Smith DGA, Vanommeslaeghe K, Mackerell AD, Merz KM, C Sherrill D. The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions. J Chem Phys. 2017 ;147(16):161727.
2016
Xu Y, Vanommeslaeghe K, Aleksandrov A, Mackerell AD, Nilsson L. Additive CHARMM force field for naturally occurring modified ribonucleotides. J Comput Chem. 2016 ;37(10):896-912.
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.
Cardenas MG, Yu W, Beguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang S-N, Cohen J, et al. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest. 2016 ;126(9):3351-62.
2015
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.
Vanommeslaeghe K, Yang M, Mackerell AD. Robustness in the fitting of molecular mechanics parameters. J Comput Chem. 2015 ;36(14):1083-101.
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.
Kumar P, Bojarowski SA, Jarzembska KN, Domagała S, Vanommeslaeghe K, Mackerell AD, Dominiak PM. A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers. J Chem Theory Comput. 2014 ;10(4):1652-1664.
Kern NR, Lee HSun, Wu EL, Park S, Vanommeslaeghe K, Mackerell AD, Klauda JB, Jo S, Im W. Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. Biophys J. 2014 ;107(8):1885-95.
Vanommeslaeghe K, Guvench O, Mackerell AD. Molecular mechanics. Curr Pharm Des. 2014 ;20(20):3281-92.
Mallajosyula SS, Vanommeslaeghe K, Mackerell AD. Perturbation of long-range water dynamics as the mechanism for the antifreeze activity of antifreeze glycoprotein. J Phys Chem B. 2014 ;118(40):11696-706.
2013
Jung K-Y, Vanommeslaeghe K, Lanning ME, Yap JL, Gordon C, Wilder PT, Mackerell AD, Fletcher S. Amphipathic α-helix mimetics based on a 1,2-diphenylacetylene scaffold. Org Lett. 2013 ;15(13):3234-7.
Cao X, Yap JL, M Newell-Rogers K, Peddaboina C, Jiang W, Papaconstantinou HT, Jupitor D, Rai A, Jung K-Y, Tubin RP, et al. The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer. 2013 ;12(1):42.
2012
Yu W, He X, Vanommeslaeghe K, Mackerell AD. Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations. J Comput Chem. 2012 ;33(31):2451-68.
Yap JL, Cao X, Vanommeslaeghe K, Jung K-Y, Peddaboina C, Wilder PT, Nan A, Mackerell AD, W Smythe R, Fletcher S. Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors. Org Biomol Chem. 2012 ;10(15):2928-33.
E Raman P, Vanommeslaeghe K, Mackerell AD. Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. J Chem Theory Comput. 2012 ;8(10):3513-3525.
2011
Guvench O, Mallajosyula SS, E Raman P, Hatcher E, Vanommeslaeghe K, Foster TJ, Jamison FW, Mackerell AD. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. J Chem Theory Comput. 2011 ;7(10):3162-3180.