Electronic and Atomic Protein Modeling (EAPM)

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Showing 151 - 174 results of 174

2009

Protein-Ligand Interactions. A theoretical modeling.

Washington University School of Medicine(St Louis, USA)

K. Borrelli
Raman study of mechanically induced oxygenation state transition of red blood cells using optical tweezers.

Biophysical journal

S. Rao, S. Bálint, B. P. Cossins, V. Guallar, and D. Petrov
Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan.

The Journal of biological chemistry

V. Guallar, C. Lu, K. Borrelli, T. Egawa, and S-R. Yeh
Peroxide-dependent formation of a covalent link between Trp51 and the heme in cytochrome c peroxidase.

Biochemistry

Z. Pipirou, V. Guallar, J. Basran, C. L. Metcalfe, E. J. Murphy, A. R. Bottrill, S. C. Mistry, and E L. Raven

2008

Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N.

Journal of the American Chemical Society

M. A. Marti, A. Bidon-Chanal, A. Crespo, S-R. Yeh, V. Guallar, F J. Luque, and D. A. Estrin
Nitric oxide reactivity with globins as investigated through computer simulation.

Methods in enzymology

M. A. Marti, L. Capece, A. Bidon-Chanal, A. Crespo, V. Guallar, F J. Luque, and D. A. Estrin
Mapping protein electron transfer pathways with QM/MM methods.

Journal of the Royal Society, Interface / the Royal Society

V. Guallar, and F. Wallrapp
Heme electron transfer in peroxidases: the propionate e-pathway.

The journal of physical chemistry. B

V. Guallar
Electron transfer in the P450cam/PDX complex. The QM/MM e-pathway.

The journal of physical chemistry. A

F. Wallrapp, D. Masone, and V. Guallar
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

Q. Wang, J. Xia, V. Guallar, G. Krilov, and E. R. Kantrowitz

2007

A quantum-chemical picture of hemoglobin affinity.

Proceedings of the National Academy of Sciences of the United States of America

R. E. Alcantara, C. Xu, T. G. Spiro, and V. Guallar

2006

The role of the heme propionates in heme biochemistry.

Journal of inorganic biochemistry

V. Guallar, and B. Olsen
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

A. Altun, V. Guallar, R. A. Friesner, S. Shaik, and W. Thiel
Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery.

Journal of the American Chemical Society

V. Guallar, A. A. Jarzecki, R. A. Friesner, and T. G. Spiro
Hydrogen bonding pathways in human dihydroorotate dehydrogenase.

The journal of physical chemistry. B

Y. A. Small, V. Guallar, A. V. Soudackov, and S. Hammes-Schiffer

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

V. Guallar, and K. Borrelli
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.

Annual review of physical chemistry

R. A. Friesner, and V. Guallar
Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach.

Journal of computational chemistry

A. E. Cho, V. Guallar, B. J. Berne, and R. A. Friesner
Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer.

Biochemistry

Y. Song, V. Guallar, and N. A. Baker

2004

Computational modeling of the catalytic reaction in triosephosphate isomerase.

Journal of molecular biology

V. Guallar, M. Jacobson, A. McDermott, and R. A. Friesner
Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study.

Journal of the American Chemical Society

V. Guallar, and R. A. Friesner

2003

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

V. Guallar, M-H. Baik, S. J. Lippard, and R. A. Friesner

2002

Proton-transfer dynamics in the activation of cytochrome P450eryF.

Journal of the American Chemical Society

V. Guallar, D. L. Harris, V. S. Batista, and W. H. Miller
Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase.

Journal of the American Chemical Society

V. Guallar, B. F. Gherman, W. H. Miller, S. J. Lippard, and R. A. Friesner

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