G. Andrés Cisneros

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1Andrew L. Feig
1Nashaat Turkman
1Rebecca Swett
1Aleksandr Shavrin
1Ren-Shuan Liu
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We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy(More)
  • Robin Bonomi, Uday Mukhopadhyay, Aleksandr Shavrin, Hsien-Hsien Yeh, Anjoy Majhi, Sajeewa W. Dewage +10 others
  • 2015
Histone deacetylases (HDAC's) became increasingly important targets for therapy of various diseases, resulting in a pressing need to develop HDAC class- and isoform-selective inhibitors. Class IIa deacetylases possess only minimal deacetylase activity against acetylated histones, but have several other client proteins as substrates through which they(More)
AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N 1-methyl adenine (1-meA) catalyzed by AlkB after the formation of Fe IV −oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the(More)
Due to the computational cost involved, when developing a force field for new compounds, one often avoids fitting van der Waals (vdW) terms, instead relying on a general force field based on the atom type. Here, we provide a novel approach to efficiently optimize vdW terms, based on both ab initio dimer energies and condensed phase properties. The approach(More)
Clostridium difficile (C. difficile) is an opportunistic pathogen that can cause potentially lethal hospital-acquired infections. The cellular damage that it causes is the result of two large clostridial cytotoxins: TcdA and TcdB which act by glucosylating cytosolic G-proteins, mis-regulation of which induces apoptosis. TcdB is a large flexible protein that(More)
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