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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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Marti, MA
,
Bidon-Chanal A
,
Crespo A
,
Yeh SR
,
Guallar V
,
Luque FJ
,
Estrin DA
. 2008.
Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N
.
Journal of the American Chemical Society. 130(5):1688-1693.
Abstract
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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).
Abstract
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L
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.
Abstract
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Morreale, A
,
de la Cruz X
,
Meyer T
,
Gelpi JL
,
Luque FJ
,
Orozco M
. 2004.
Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
Proteins. 57(3):458-467.
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Bidon-Chanal, A
,
Marti MA
,
Crespo A
,
Milani M
,
Orozco M
,
Bolognesi M
,
Luque FJ
,
Estrin DA
. 2006.
Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N
.
Proteins. 64(2):457-464.
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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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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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Forti, F
,
Boechi L
,
Bikiel D
,
Marti MA
,
Nardini M
,
Bolognesi M
,
Viappiani C
,
Estrin D
,
Luque FJ
. 2011.
Ligand Migration in Methanosarcina acetivorans Protoglobin: Effects of Ligand Binding and Dimeric Assembly
.
The journal of physical chemistry.B.
Abstract
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K
Oliveira, A
,
Allegri A
,
Bidon-Chanal A
,
Knipp M
,
Roitberg A
,
Abbruzzetti S
,
Viappiani C
,
Luque FJ
. 2013.
Kinetics and computational studies of ligand migration in nitrophorin 7 and its Delta1-3 mutant
.
Biochimica Biophysica Acta – Proteins Proteinomics. 1834:1711-1721.
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I
Cubero, E
,
Luque FJ
,
Orozco M
. 1998.
Is polarization important in cation-pi interactions?
Proceedings of the National Academy of Sciences of the United States of America. 95(11):5976-5980.
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Soteras, I
,
Orozco M
,
Luque FJ
. 2008.
Induction effects in metal cation-benzene complexes
.
Physical chemistry chemical physics : PCCP. 10(19):2616-2624.
Abstract
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Noy, A
,
Soteras I
,
Luque FJ
,
Orozco M
. 2009.
The impact of monovalent ion force field model in nucleic acids simulations
.
Physical chemistry chemical physics : PCCP. 11(45):10596-10607.
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H
Munoz, J
,
Barril X
,
Hernandez B
,
Orozco M
,
Luque FJ
. 2002.
Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index
.
Journal of computational chemistry. 23(5):554-563.
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Munoz-Muriedas, J
,
Barril X
,
Lopez JM
,
Orozco M
,
Luque FJ
. 2007.
A hydrophobic similarity analysis of solvation effects on nucleic acid bases
.
Journal of molecular modeling. 13(2):357-365.
Abstract
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Munoz-Muriedas, J
,
Perspicace S
,
Bech N
,
Guccione S
,
Orozco M
,
Luque FJ
. 2005.
Hydrophobic molecular similarity from MST fractional contributions to the octanol/water partition coefficient
.
Journal of computer-aided molecular design. 19(6):401-419.
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Galdeano, C
,
Viayna E
,
Sola I
,
Formosa X
,
Camps P
,
Badia A
,
Clos MV
,
Relat J
,
Ratia M
,
Bartolini M
et al.
. 2012.
Huprine–Tacrine Heterodimers as Anti-Amyloidogenic Compounds of Potential Interest against Alzheimer’s and Prion Diseases
.
J. Med. Chem. . 55
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Cubero, E
,
Avino A
,
de la Torre BG
,
Frieden M
,
Eritja R
,
Luque FJ
,
Gonzalez C
,
Orozco M
. 2002.
Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives
.
Journal of the American Chemical Society. 124(12):3133-3142.
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Spyrakis, F
,
Faggiano S
,
Abbruzzetti S
,
Dominici P
,
Cacciatori E
,
Astegno A
,
Droghetti E
,
Feis A
,
Smulevich G
,
Bruno S
et al.
. 2011.
Histidine E7 dynamics modulates ligand exchange between distal pocket and solvent in AHb1 from Arabidopsis thaliana
.
The journal of physical chemistry.B. 115(14):4138-4146.
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Capece, L
,
Marti MA
,
Bidon-Chanal A
,
Nadra A
,
Luque FJ
,
Estrin DA
. 2009.
High pressure reveals structural determinants for globin hexacoordination: neuroglobin and myoglobin cases
.
Proteins. 75(4):885-894.
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Aleman, C
,
Roca R
,
Luque FJ
,
Orozco M
. 1997.
Helical preferences of alanine, glycine, and aminoisobutyric homopeptides
.
Proteins. 28(1):83-93.
Abstract
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G
Svozil, D
,
Sponer JE
,
Marchan I
,
Perez A
,
3rd CTE
,
Forti F
,
Luque FJ
,
Orozco M
,
Sponer J
. 2008.
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids
.
The journal of physical chemistry.B. 112(27):8188-8197.
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Rueda, M
,
Luque FJ
,
Orozco M
. 2006.
G-quadruplexes can maintain their structure in the gas phase
.
Journal of the American Chemical Society. 128(11):3608-3619.
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F
Perez, A
,
Luque FJ
,
Orozco M
. 2012.
Frontiers in Molecular Dynamics Simulations of DNA
.
Acc. Chem. Res.. 45
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Luque, FJ
,
Barril X
,
Orozco M
. 1999.
Fractional description of free energies of solvation
.
Journal of computer-aided molecular design. 13(2):139-152.
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