QM/MM

Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: Quantum mechanical/molecular mechanical free energy simulations

188. S. Zhang, A. Ganguly, P. Goyal, J. Bingamin, P. C. Bevilacqua, and S. Hammes-Schiffer, “Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: Quantum mechanical/molecular mechanical free energy simulations,”J. Am. Chem. Soc. 137, 784-798 (2015).

Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme

173. A. Ganguly, P. Thaplyal, E. Rosta, P. C. Bevilacqua, and S. Hammes-Schiffer, “Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme,” J. Am. Chem. Soc. 136, 1483-1496 (2014).

Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme

170. P. Thaplyal, A. Ganguly, B. L. Golden, and S. Hammes-Schiffer, “Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme,” Biochemistry 52, 6499-6514 (2013).

Identification of the catalytic Mg2+ ion in the hepatitis delta virus ribozyme

162. J. Chen, A. Ganguly, Z. Miswan, S. Hammes-Schiffer, P. C. Bevilacqua, and B. L. Golden, “Identification of the catalytic Mg2+ ion in the hepatitis delta virus ribozyme, ” Biochemistry 52, 557-567 (2013).

Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism

150. A. Ganguly, P. C. Bevilacqua, and S. Hammes-Schiffer, “Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism,” J. Phys. Chem. Lett. 2, 2906-2911 (2011).