IBBR Publications

Mackerell AD, Jo S, Lakkaraju SKaushik, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj. 2020 ;1864(4):129519.

Ustach VD, Lakkaraju SKaushik, Jo S, Yu W, Jiang W, Mackerell AD. Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. J Chem Inf Model. 2019 .

Sun D, Lakkaraju SKaushik, Jo S, Mackerell AD. Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water. J Chem Theory Comput. 2018 .

Yu W, Jo S, Lakkaraju SKaushik, Weber DJ, Mackerell AD. Exploring protein-protein interactions using the Site-Identification by Ligand Competitive Saturation (SILCS) methodology. Proteins. 2018 .

Jo S, Cheng X, Lee J, Kim S, Park S-J, Patel DS, Beaven AH, Lee KIl, Rui H, Park S, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem. 2017 ;38(15):1114-1124.

Lee J, Cheng X, Swails JM, Yeom MSun, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JCheol, Qi Y, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J Chem Theory Comput. 2016 ;12(1):405-13.

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.

Mallajosyula SS, Jo S, Im W, Mackerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods Mol Biol. 2015 ;1273:407-29.

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.

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.

Jo S, Song KC, Desaire H, Mackerell AD, Im W. Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J Comput Chem. 2011 ;32(14):3135-41.