Electronic and Atomic Protein Modeling (EAPM)

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Showing 121 - 150 results of 174

2013

Molecular Interactions of Prodiginines with the BH3 Domain of Anti-Apoptotic Bcl-2 Family Members.

PloS one

A. Hosseini, M. Espona-Fiedler, V. Soto-Cerrato, R. Quesada, R. Pérez-Tomás, and V. Guallar
Direct observation of single DNA structural alterations at low forces with surface-enhanced Raman scattering.

Biophysical journal

S. Rao, S. Raj, B. Cossins, M. Marro, V. Guallar, and D. Petrov
Single vs. multiple ligand pathways in globins: A computational view.

Biochimica et biophysica acta

F. M. Lucas, and V. Guallar

2012

Cisplatin, still a long way to go

TACC-2012, Theory and Applications in Computational Chemistry. Pavia, Lombardia, Italy

F. M. Lucas
Dynamical mapping of Protein-Protein Interactions

Universitat de Barcelona

D. Masone
Ligand migration in Globins

International Conference on Oxygen Binding and Sensing Proteins (O2BiP), Parma, (Italy)

V. Guallar
PELE: Low Cost Protein-Ligand Dynamics and Induced Fit

Structural & Computational Chemistry, Discovery Congress Chemistry, Munich (Germany)

V. Guallar
Mapping ligand dynamics pathways in globin systems

II International BIC Symposium, University of Canterbury, ChristChurch, New Zealand

V. Guallar
DESMOND European hands-on workshop

2012
Using QM/MM Methods for the Exploration of Electron Transfer Pathways

Current Inorganic Chemistry

F. Lucas, D. Masone, S. Saen-oon, F. Wallrapp, and V. Guallar
Exploration of Protein Conformational Change with PELE and Meta-Dynamics

Journal of Chemical Theory and Computation

B. P. Cossins, A. Hosseini, and V. Guallar
Role of active site histidines in the two half-reactions of the aryl-alcohol oxidase catalytic cycle.

Biochemistry

A. Hernández-Ortega, F. Lucas, P. Ferreira, M. Medina, V. Guallar, and A. T. Martínez
Characterization of adenosine receptor in its native environment: insights from molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B) adenosine receptor.

Journal of molecular modeling

A. Madadkar-Sobhani
Two tyrosyl radicals stabilize high oxidation States in cytochrome C oxidase for efficient energy conservation and proton translocation.

Journal of the American Chemical Society

M. A. Yu, T. Egawa, K. Shinzawa-Itoh, S. Yoshikawa, V. Guallar, S-R. Yeh, D. L. Rousseau, and G. J. Gerfen
An atomistic view on human hemoglobin carbon monoxide migration processes.

Biophysical journal

F. M. Lucas, and V. Guallar
Identification of dual mTORC1 and mTORC2 inhibitors in melanoma cells: Prodigiosin vs. obatoclax.

Biochemical pharmacology

M. Espona-Fiedler, V. Soto-Cerrato, A. Hosseini, J. M. Lizcano, V. Guallar, R. Quesada, T. Gao, and R. Pérez-Tomás
Stereoselective Hydride Transfer by Aryl-Alcohol Oxidase, a Member of the GMC Superfamily.

Chembiochem : a European journal of chemical biology

A. Hernández-Ortega, P. Ferreira, P. Merino, M. Medina, V. Guallar, and A. T. Martínez

2011

Mixed Quantum and classical simulation techniques for zapping eletron transfer in proteins

Universitat Pompeu Fabra

F. Wallrap
Induced Fit Modelling with Monte Carlo techniques: protein Energy Landscape Exploration

11th Structure based Drug design (SBDD), Boston (USA)

V. Guallar
Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase.

The Biochemical journal

A. Hernández-Ortega, K. Borrelli, P. Ferreira, M. Medina, A. T. Martínez, and V. Guallar
Regulation of electron and proton transfer by the protein matrix of cytochrome c oxidase.

The journal of physical chemistry. B

V. Daskalakis, S. C. Farantos, V. Guallar, and C. Varotsis
Electron transfer pathways in cytochrome c oxidase.

Biochimica et biophysica acta

F. M. Lucas, D. L. Rousseau, and V. Guallar
A new view of the bacterial cytosol environment.

PLoS computational biology

B. P. Cossins, M. P. Jacobson, and V. Guallar
Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine.

The Journal of biological chemistry

A. Hernández-Ortega, F. Lucas, P. Ferreira, M. Medina, V. Guallar, and A. T. Martínez
H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough?

Proteins

D. Masone, I. Cabeza de Vaca, C. Pons, J. Fernández-Recio, and V. Guallar

2010

QM/MM e-pathway: mapping Electron transfer processes in proteins

ACS National Meeting –San Franciscisco(USA

F. Wallrap
QM/MM methods: looking inside heme proteins biochemistry.

Biophysical chemistry

V. Guallar, and F. H. Wallrapp
Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility.

Journal of computational chemistry

K. Borrelli, B. P. Cossins, and V. Guallar
Vibrational resonances and CuB displacement controlled by proton motion in cytochrome c oxidase.

The journal of physical chemistry. B

V. Daskalakis, S. C. Farantos, V. Guallar, and C. Varotsis
QM/MM methods: looking inside heme proteins biochemistry.

Biophysical chemistry

V. Guallar, and F. Wallrapp

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