IBBR Publications

Yu W, Mackerell AD. Computer-Aided Drug Design Methods. Methods Mol Biol. 2017 ;1520:85-106.

Cardenas MG, Oswald E, Yu W, Xue F, Mackerell AD, Melnick AM. The Expanding Role of the BCL6 Oncoprotein as a Cancer Therapeutic Target. Clin Cancer Res. 2017 ;23(4):885-893.

Liang D, Yu W, Nguyen N, Deschamps JR, Imler GH, Li Y, Mackerell AD, Jiang C, Xue F. Iodobenzene-Catalyzed Synthesis of Phenanthridinones via Oxidative C-H Amidation. J Org Chem. 2017 ;82(7):3589-3596.

Sarkar A, Yu W, Desai UR, Mackerell AD, Mosier PD. Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction. Glycobiology. 2016 ;26(10):1041-1047.

Heinzl GA, Huang W, Yu W, Giardina BJ, Zhou Y, Mackerell AD, Wilks A, Xue F. Iminoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa. J Med Chem. 2016 ;59(14):6929-42.

Cavalier MC, Melville Z, Aligholizadeh E, E Raman P, Yu W, Fang L, Alasady M, Pierce AD, Wilder PT, Mackerell AD, et al. Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography. Acta Crystallogr D Struct Biol. 2016 ;72(Pt 6):753-60.

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.

Lanning ME, Yu W, Yap JL, Chauhan J, Chen L, Whiting E, Pidugu LS, Atkinson T, Bailey H, Li W, et al. Structure-based design of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoates as selective inhibitors of the Mcl-1 oncoprotein. Eur J Med Chem. 2016 ;113:273-92.

Yang W, Sun X, Yu W, Rai R, Deschamps JR, Mitchell LA, Jiang C, Mackerell AD, Xue F. Facile Synthesis of Spirocyclic Lactams from β-Keto Carboxylic Acids. Org Lett. 2015 ;17(12):3070-3.

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.

Fletcher S, Yu W, Huang J, Kwasny SM, Chauhan J, Opperman TJ, Mackerell AD, de Leeuw EPH. Structure-activity exploration of a small-molecule Lipid II inhibitor. Drug Des Devel Ther. 2015 ;9:2383-94.

Lakkaraju SKaushik, E Raman P, Yu W, Mackerell AD. Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations. J Chem Theory Comput. 2014 ;10(6):2281-2290.

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.

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.

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.

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.

Varney KM, Bonvin AMJJ, Pazgier M, Malin J, Yu W, Ateh E, Oashi T, Lu W, Huang J, de Buin MDiepeveen-, et al. Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II. PLoS Pathog. 2013 ;9(11):e1003732.

Yu W, Wu Z, Chen H, Liu X, Mackerell AD, Lin Z. Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures. J Phys Chem B. 2012 ;116(7):2269-83.

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.

E Raman P, Yu W, Guvench O, Mackerell AD. Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. J Chem Inf Model. 2011 ;51(4):877-96.

Xu Z, Chen Y-W, Battu A, Wilder P, Weber DJ, Yu W, Mackerell AD, Chen L-M, Chai KX, Johnson MD, et al. Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade. J Med Chem. 2011 ;54(21):7567-78.