IBBR Publications

Found 67 results
Filters: Keyword is Models, Chemical  [Clear All Filters]
2015
Savelyev A, Mackerell AD. Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields. J Phys Chem B. 2015 ;119(12):4428-40.
Lakkaraju SK, Mbatia H, Hanscom M, Zhao Z, Wu J, Stoica B, Mackerell AD, Faden AI, Xue F. Cyclopropyl-containing positive allosteric modulators of metabotropic glutamate receptor subtype 5. Bioorg Med Chem Lett. 2015 ;25(11):2275-9.
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.
Vanommeslaeghe K, Yang M, Mackerell AD. Robustness in the fitting of molecular mechanics parameters. J Comput Chem. 2015 ;36(14):1083-101.
2014
Savelyev A, Mackerell AD. All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem. 2014 ;35(16):1219-39.
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
Taraban MB, Hyland LL, Y Yu B. Split of chiral degeneracy in mechanical and structural properties of oligopeptide-polysaccharide biomaterials. Biomacromolecules. 2013 ;14(9):3192-201.
Sandineni A, Lin B, Mackerell AD, Cho BP. Structure and thermodynamic insights on acetylaminofluorene-modified deletion DNA duplexes as models for frameshift mutagenesis. Chem Res Toxicol. 2013 ;26(6):937-51.
Healy JR, Bezawada P, Shim J, Jones JW, Kane MA, Mackerell AD, Coop A, Matsumoto RR. Synthesis, modeling, and pharmacological evaluation of UMB 425, a mixed μ agonist/δ antagonist opioid analgesic with reduced tolerance liabilities. ACS Chem Neurosci. 2013 ;4(9):1256-66.
2012
Vanommeslaeghe K, E Raman P, Mackerell AD. Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J Chem Inf Model. 2012 ;52(12):3155-68.
Suhasini AN, Sommers JA, Yu S, Wu Y, Xu T, Kelman Z, Kaplan DL, Brosh RM. DNA repair and replication fork helicases are differentially affected by alkyl phosphotriester lesion. J Biol Chem. 2012 ;287(23):19188-98.
2011
Krueger S, Shin J-H, Raghunandan S, Curtis JE, Kelman Z. Atomistic ensemble modeling and small-angle neutron scattering of intrinsically disordered protein complexes: applied to minichromosome maintenance protein. Biophys J. 2011 ;101(12):2999-3007.
Baker CM, Anisimov VM, Mackerell AD. Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. J Phys Chem B. 2011 ;115(3):580-96.
Mallajosyula SS, Mackerell AD. Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides. J Phys Chem B. 2011 ;115(38):11215-29.
Walker ML, Vanderah DJ, Rubinson KA. In-situ characterization of self-assembled monolayers of water-soluble oligo(ethylene oxide) compounds. Colloids Surf B Biointerfaces. 2011 ;82(2):450-5.
2010
E Raman P, Guvench O, Mackerell AD. CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. J Phys Chem B. 2010 ;114(40):12981-94.
Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, et al. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010 ;31(4):671-90.
Ballin JD, Prevas JP, Ross CR, Toth EA, Wilson GM, M Record T. Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH. Biochemistry. 2010 ;49(9):2018-30.
Zhu X, Mackerell AD. Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model. J Comput Chem. 2010 ;31(12):2330-41.
2009
Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009 ;30(10):1545-614.
Mackerell AD. Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA. J Phys Chem B. 2009 ;113(10):3235-44.
Lee H-W, Briggs KT, Marino JP. Dissecting structural transitions in the HIV-1 dimerization initiation site RNA using 2-aminopurine fluorescence. Methods. 2009 ;49(2):118-27.
2008
Guvench O, Greene SN, Kamath G, Brady JW, Venable RM, Pastor RW, Mackerell AD. Additive empirical force field for hexopyranose monosaccharides. J Comput Chem. 2008 ;29(15):2543-64.
Guvench O, Mackerell AD. Automated conformational energy fitting for force-field development. J Mol Model. 2008 ;14(8):667-79.
Acharya C, Seo PR, Polli JE, Mackerell AD. Computational model for predicting chemical substituent effects on passive drug permeability across parallel artificial membranes. Mol Pharm. 2008 ;5(5):818-28.