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Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase. Journal of the American Chemical Society 124, 3377-84 (2002).
Proton-transfer dynamics in the activation of cytochrome P450eryF. Journal of the American Chemical Society 124, 1430-7 (2002).
Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450. Proceedings of the National Academy of Sciences of the United States of America 100, 6998-7002 (2003).
Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of molecular biology 337, 227-39 (2004).
Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study. Journal of the American Chemical Society 126, 8501-8 (2004).
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annual review of physical chemistry 56, 389-427 (2005).
A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding. Proceedings of the National Academy of Sciences of the United States of America 102, 3954-9 (2005).
Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. Journal of computational chemistry 26, 915-31 (2005).
The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM study. Journal of the American Chemical Society 128, 3924-5 (2006).
Hydrogen bonding pathways in human dihydroorotate dehydrogenase. The journal of physical chemistry. B 110, 19704-10 (2006).
Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery. Journal of the American Chemical Society 128, 5427-35 (2006).
The role of the heme propionates in heme biochemistry. Journal of inorganic biochemistry 100, 755-60 (2006).
A quantum-chemical picture of hemoglobin affinity. Proceedings of the National Academy of Sciences of the United States of America 104, 18451-5 (2007).
Electron transfer in the P450cam/PDX complex. The QM/MM e-pathway. The journal of physical chemistry. A 112, 12989-94 (2008).
Heme electron transfer in peroxidases: the propionate e-pathway. The journal of physical chemistry. B 112, 13460-4 (2008).
Mapping protein electron transfer pathways with QM/MM methods. Journal of the Royal Society, Interface / the Royal Society 5 Suppl 3, S233-9 (2008).
Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N. Journal of the American Chemical Society 130, 1688-93 (2008).
Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases. Proceedings of the National Academy of Sciences of the United States of America 105, 16918-23 (2008).
Nitric oxide reactivity with globins as investigated through computer simulation. Methods in enzymology 437, 477-98 (2008).
Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan. The Journal of biological chemistry 284, 3106-16 (2009).
Peroxide-dependent formation of a covalent link between Trp51 and the heme in cytochrome c peroxidase. Biochemistry 48, 3593-9 (2009).
Raman study of mechanically induced oxygenation state transition of red blood cells using optical tweezers. Biophysical journal 96, 209-16 (2009).
Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility. Journal of computational chemistry 31, 1224-35 (2010).
QM/MM methods: looking inside heme proteins biochemistry. Biophysical chemistry 149, 1-11 (2010).
Vibrational resonances and CuB displacement controlled by proton motion in cytochrome c oxidase. The journal of physical chemistry. B 114, 1136-43 (2010).
Electron transfer pathways in cytochrome c oxidase. Biochimica et biophysica acta 1807, 1305-13 (2011).
H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough?. Proteins (2011).doi:10.1002/prot.23239
Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine. The Journal of biological chemistry 286, 41105-14 (2011).
A new view of the bacterial cytosol environment. PLoS computational biology 7, e1002066 (2011).
Regulation of electron and proton transfer by the protein matrix of cytochrome c oxidase. The journal of physical chemistry. B 115, 3648-55 (2011).
Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase. The Biochemical journal 436, 341-50 (2011).
An atomistic view on human hemoglobin carbon monoxide migration processes. Biophysical journal 102, 887-96 (2012).
Exploration of Protein Conformational Change with PELE and Meta-Dynamics. Journal of Chemical Theory and Computation 8, 959-965 (2012).
H-bond network optimization in protein-protein complexes: are all-atom force field scores enough?. Proteins 80, 818-24 (2012).
Identification of dual mTORC1 and mTORC2 inhibitors in melanoma cells: Prodigiosin vs. obatoclax. Biochemical pharmacology 83, 489-96 (2012).
Role of active site histidines in the two half-reactions of the aryl-alcohol oxidase catalytic cycle. Biochemistry 51, 6595-608 (2012).
Stereoselective Hydride Transfer by Aryl-Alcohol Oxidase, a Member of the GMC Superfamily. Chembiochem : a European journal of chemical biology (2012).doi:10.1002/cbic.201100709
Direct observation of single DNA structural alterations at low forces with surface-enhanced Raman scattering. Biophysical journal 104, 156-62 (2013).
Molecular Interactions of Prodiginines with the BH3 Domain of Anti-Apoptotic Bcl-2 Family Members. PloS one 8, e57562 (2013).