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Journal Article
Abbruzzetti, S
,
Spyrakis F
,
BidonChanal A
,
Luque FJ
,
Viappiani C
. 2013.
Ligand migration through hemeprotein cavities: Insights from laser flash photolysis and molecular dynamics simulations
.
Physical Chemistry Chemical Physics. 15:10686-10701.
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Fradera, X
,
Cruz D LX
,
Silva CH
,
Gelpi JL
,
Luque FJ
,
Orozco M
. 2002.
Ligand-induced changes in the binding sites of proteins
.
Bioinformatics (Oxford, England). 18(7):939-948.
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Huertas, O
,
Poater J
,
Fuentes-Cabrera M
,
Orozco M
,
Sola M
,
Luque FJ
. 2006.
Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives
.
The journal of physical chemistry.A. 110(44):12249-12258.
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Schmidtke, P
,
Bidon-Chanal A
,
Luque FJ
,
Barril X
. 2011.
MDpocket : Open Source Cavity Detection and Characterization on Molecular Dynamics Trajectories
.
Bioinformatics (Oxford, England).
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Kim, J
,
Huxter VM
,
Curutchet C
,
Scholes GD
. 2009.
Measurement of Electron-Electron Interactions and Correlations Using Two-Dimensional Electronic Double-Quantum Coherence Spectroscopy
.
Journal of Physical Chemistry A. 113(44):12122-12133.
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Singh, S
,
Thakur N
,
Oliveira A
,
Petruk AA
,
Hade MD
,
Sethi D
,
Bidon-Chanal A
,
Marti MA
,
Datta H
,
Parkesh R
et al.
. 2014.
Mechanistic insight into the enzymatic reduction of truncated hemoglobin N of Mycobacterium tuberculosis: Role of the CD loop and Pre-A motif in electron cycling
.
Journal of Biological Chemistry. 289
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Hernandez, B
,
Soliva R
,
Luque FJ
,
Orozco M
. 2000.
Misincorporation of 2'-deoxyoxanosine into DNA: a molecular basis for NO-induced mutagenesis derived from theoretical calculations
.
Nucleic acids research. 28(24):4873-4883.
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Fradera, X
,
Marquez M
,
Smith BD
,
Orozco M
,
Luque FJ
. 2003.
Molecular dynamics study of 2rotaxanes: influence of solvation and cation on co-conformation
.
The Journal of organic chemistry. 68(12):4663-4673.
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Barril, X
,
Soliva R
. 2006.
Molecular modelling
.
Molecular bioSystems. 2(12):660-681.
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Curutchet, C
,
Bidon-Chanal A
,
Soteras I
,
Orozco M
,
Luque FJ
. 2005.
MST continuum study of the hydration free energies of monovalent ionic species
.
Journal of Physical Chemistry B. 109(8):3565-3574.
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Sponer, J
,
Jurecka P
,
Marchan I
,
Luque FJ
,
Orozco M
,
Hobza P
. 2006.
Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
.
Chemistry (Weinheim an der Bergstrasse, Germany). 12(10):2854-2865.
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Zgarbova, M
,
Luque FJ
,
Sponer J
,
Otyepka M
,
Jurecka P
. 2012.
A novel approach for deriving force field torsion angle parameters accounting for conformation-dependent solvation effects
.
J. Chem. Theory Comput.. 8:3242.
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Camps, P
,
Formosa X
,
Galdeano C
,
Gomez T
,
Munoz-Torrero D
,
Scarpellini M
,
Viayna E
,
Badia A
,
Clos MV
,
Camins A
et al.
. 2008.
Novel donepezil-based inhibitors of acetyl- and butyrylcholinesterase and acetylcholinesterase-induced beta-amyloid aggregation
.
Journal of medicinal chemistry. 51(12):3588-3598.
Abstract
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Dymock, BW
,
Barril X
,
Brough PA
,
Cansfield JE
,
Massey A
,
McDonald E
,
Hubbard RE
,
Surgenor A
,
Roughley SD
,
Webb P
et al.
. 2005.
Novel, potent small-molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design
.
Journal of medicinal chemistry. 48(13):4212-4215.
Abstract
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Eccles, SA
,
Massey A
,
Raynaud FI
,
Sharp SY
,
Box G
,
Valenti M
,
Patterson L
,
de Brandon HA
,
Gowan S
,
Boxall F
et al.
. 2008.
NVP-AUY922: a novel heat shock protein 90 inhibitor active against xenograft tumor growth, angiogenesis, and metastasis
.
Cancer research. 68(8):2850-2860.
Abstract
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Soteras, I
,
Lozano O
,
Gomez-Esque A
,
Escolano C
,
Orozco M
,
Amat M
,
Bosch J
,
Luque FJ
. 2006.
On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates
.
Journal of the American Chemical Society. 128(20):6581-6588.
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Luisi, B
,
Orozco M
,
Sponer J
,
Luque FJ
,
Shakked Z
. 1998.
On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules
.
Journal of Molecular Biology. 279(5):1123-1136.
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Spyrakis, F
,
Bruno S
,
Bidon-Chanal A
,
Luque FJ
,
Abbruzzetti S
,
Viappiani C
,
Dominici P
,
Mozzarelli A
. 2011.
Oxygen binding to Arabidopsis thaliana AHb2 nonsymbiotic hemoglobin: evidence for a role in oxygen transport
.
IUBMB life. 63(5):355-362.
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Soteras, I
,
Forti F
,
Orozco M
,
Luque FJ
. 2009.
Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies
.
The journal of physical chemistry.B. 113(27):9330-9334.
Abstract
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Soteras, I
,
Orozco M
,
Luque FJ
. 2010.
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies
.
Journal of computer-aided molecular design. 24(4):281-291.
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Curutchet, C
,
Kongsted J
,
Munoz-Losa A
,
Hossein-Nejad H
,
Scholes GD
,
Mennucci B
. 2011.
Photosynthetic Light-Harvesting Is Tuned by the Heterogeneous Polarizable Environment of the Protein
.
Journal of the American Chemical Society. 133(9):3078-3084.
Abstract
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Spyrakis, F
,
BidonChanal A
,
Barril X
,
Luque FJ
. 2011.
Protein flexibility and ligand recognition: challenges for molecular modeling
.
Current topics in medicinal chemistry. 11(2):192-210.
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Ruiz-Carmona, S
,
Alvarez-garcia D
,
Foloppe N
,
a Garmendia-Doval B
,
Juhos S
,
Schmidtke P
,
Barril X
,
Hubbard RE
,
Morley DS
. 2014.
rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids.
.
PLoS computational biology. 10(4):e1003571-e1003571.
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Andrews, DL
,
Curutchet C
,
Scholes GD
. 2011.
Resonance energy transfer: Beyond the limits
.
Laser & Photonics Reviews. 5(1):114-123.
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Oliveira, A
,
Singh S
,
Bidon-Chanal A
,
Forti F
,
Marti MA
,
Boechi L
,
Estrin DA
,
Dikshit KL
,
Luque FJ
. 2012.
Role of PheE15 Gate in Ligand Entry and Nitric Oxide Detoxification Function of Mycobacterium tuberculosis Truncated Hemoglobin N
.
PLoS ONE. 7
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