IBBR Publications
Found 67 results
Filters: Keyword is Models, Chemical [Clear All Filters]
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.
. Cyclopropyl-containing positive allosteric modulators of metabotropic glutamate receptor subtype 5. Bioorg Med Chem Lett. 2015 ;25(11):2275-9.
. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. J Chem Inf Model. 2015 ;55(2):407-20.
. Robustness in the fitting of molecular mechanics parameters. J Comput Chem. 2015 ;36(14):1083-101.
. All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem. 2014 ;35(16):1219-39.
. Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. J Comput Aided Mol Des. 2014 ;28(5):491-507.
. Split of chiral degeneracy in mechanical and structural properties of oligopeptide-polysaccharide biomaterials. Biomacromolecules. 2013 ;14(9):3192-201.
. Structure and thermodynamic insights on acetylaminofluorene-modified deletion DNA duplexes as models for frameshift mutagenesis. Chem Res Toxicol. 2013 ;26(6):937-51.
. 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.
. 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.
. DNA repair and replication fork helicases are differentially affected by alkyl phosphotriester lesion. J Biol Chem. 2012 ;287(23):19188-98.
. 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.
. 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.
. Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides. J Phys Chem B. 2011 ;115(38):11215-29.
. In-situ characterization of self-assembled monolayers of water-soluble oligo(ethylene oxide) compounds. Colloids Surf B Biointerfaces. 2011 ;82(2):450-5.
. CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. J Phys Chem B. 2010 ;114(40):12981-94.
. 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.
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.
. Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model. J Comput Chem. 2010 ;31(12):2330-41.
. CHARMM: the biomolecular simulation program. J Comput Chem. 2009 ;30(10):1545-614.
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.
. Dissecting structural transitions in the HIV-1 dimerization initiation site RNA using 2-aminopurine fluorescence. Methods. 2009 ;49(2):118-27.
. Additive empirical force field for hexopyranose monosaccharides. J Comput Chem. 2008 ;29(15):2543-64.
. Automated conformational energy fitting for force-field development. J Mol Model. 2008 ;14(8):667-79.
. .