IBBR Publications

Found 139 results
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Lin B, He X, Mackerell AD. A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields. J Phys Chem B. 2013 ;117(36):10572-80.
McDonald ARinger, Denning EJ, Mackerell AD. Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA. J Phys Chem A. 2013 ;117(7):1560-8.
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.
Lin B, Lopes PEM, Roux B, Mackerell AD. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. J Chem Phys. 2013 ;139(8):084509.
Chowdhary J, Harder E, Lopes PEM, Huang L, Mackerell AD, Roux B. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B. 2013 ;117(31):9142-60.
E Raman P, Mackerell AD. Rapid estimation of hydration thermodynamics of macromolecular regions. J Chem Phys. 2013 ;139(5):055105.
Jain V, Hilton B, Lin B, Jain A, Mackerell AD, Zou Y, Cho BP. Structural and thermodynamic insight into Escherichia coli UvrABC-mediated incision of cluster diacetylaminofluorene adducts on the NarI sequence. Chem Res Toxicol. 2013 ;26(8):1251-62.
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.
Jain V, Hilton B, Lin B, Patnaik S, Liang F, Darian E, Zou Y, Mackerell AD, Cho BP. Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor. Nucleic Acids Res. 2013 ;41(2):869-80.