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M
Munoz-Muriedas, J, Lopez JM, Orozco M, Luque FJ.  2004.  Molecular modelling approaches to the design of acetylcholinesterase inhibitors: new challenges for the treatment of Alzheimer's disease. Current pharmaceutical design. 10(25):3131-3140. Abstract
Cardenas, C, Bidon-Chanal A, Conejeros P, Arenas G, Marshall S, Luque FJ.  2010.  Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar. Journal of computer-aided molecular design. 24(12):1035-1051. Abstract
van Gunsteren, WF, Luque FJ, Timms D, Torda AE.  1994.  Molecular mechanics in biology: from structure to function, taking account of solvation. Annual Review of Biophysics and Biomolecular Structure. 23:847-863.
Alhambra, C, Luque FJ, Portugal J, Orozco M.  1995.  Molecular dynamics study of the binding of elsamicin A to DNA. European journal of biochemistry / FEBS. 230(2):555-566. Abstract
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. Abstract
Llabres, S, Garcia-Rafes S, Cristobal-Lecina E, Riera A, Borrell JI, Camarasa J, Pubill D, Luque FJ, Escubedo E.  2014.  Molecular basis of the selective binding of MDMA enantiomers to the alpha4beta2 nicotinic receptor subtype: Synthesis, pharmacological evaluation and mechanistic studies. European Journal of Medicinal Chemistry. 81
Martin-Santamaria, S, Munoz-Muriedas J, Luque FJ, Gago F.  2004.  Modulation of binding strength in several classes of active site inhibitors of acetylcholinesterase studied by comparative binding energy analysis. Journal of medicinal chemistry. 47(18):4471-4482. Abstract
Hernandez, B, Luque FJ, Orozco M.  2000.  Mixed QM/MM molecular electrostatic potentials. Journal of computer-aided molecular design. 14(4):329-339. Abstract
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. Abstract
Perissinotti, LL, Marti MA, Doctorovich F, Luque FJ, Estrin DA.  2008.  A microscopic study of the deoxyhemoglobin-catalyzed generation of nitric oxide from nitrite anion. Biochemistry. 47(37):9793-9802. Abstract
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
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
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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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
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. Abstract
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. Abstract
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. Abstract
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.
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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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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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. Abstract
Soteras, I, Orozco M, Luque FJ.  2008.  Induction effects in metal cation-benzene complexes. Physical chemistry chemical physics : PCCP. 10(19):2616-2624. Abstract
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. Abstract
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. Abstract
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