-2015-

I. Sánchez-Moreno, I. Bordes, R. Castillo, J.J. Ruiz-Pernía, V. Moliner, E. García-Junceda "Tuning the Phosphoryl Donor Specificity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate. An Insight from Computational Studies"  Int. J. Mol. Sci. 16, 27835-27849 (2015) DOI: 10.3390/ijms161126073

I. Bordes, J. Recatá, K. Świderek, V. Moliner "Is Promiscuous CALB a Good Scaffold for Designing New Epoxidases" 
Molecules 20,17789-17806 (2015) DOI: 10.3390/molecules201017789

K. Świderek, S. Martí, I. Tuñon, V. Moliner, J. Bertran, "Peptide Bond Formation Mechanism Catalyzed by Ribosome." J. Am. Chem. Soc. 137, 12024-12034 (2015) DOI: 10.1021/jacs.5b05916

I. Bordes, J.J. Pernia, R. Castillo, V. Moliner "A Computational Study of the Phosphoryl Transfer Reaction between ATP and Dha in Aqueous Solution" 
Org. Biomol. Chem., 2015 (Just Accepted) DOI: 10.1039/C5OB01079A

I. Viciano, R. Castillo, S. Martí "QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1)" 
J. Comput. Chem. 36, 1736–1747, (2015) DOI: 10.1002/jcc.23967

L.Y.P. Luk, J.J. Ruiz-Pernía, A.S. Adesina, E.J. Loveridge, I. Tuñón, V. Moliner, R. K. Allemann "Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase." Angew. Chem. Int. Ed. 54, 9016–9020, (2015) DOI: 10.1002/anie.201503968

K. Arafet, S. Ferrer, V. Moliner "First QM/MM Studies of Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones" Biochemistry, 54, 3381–3391 (2015) DOI: 10.1021/bi501551g

K. Świderek, A. Kohen, V. Moliner "Influence of Active Site Conformations on the Hydride Transfer step of the Thymidylate Synthase Reaction Mechanism" 
Phys. Chem. Chem. Phys. 17, 30793-30804 (2015) DOI: 10.1039/C5CP01239B

A. de la Lande, V. Moliner, D. Salahub "Measurement and prediction of quantum coherence effects in biological processes" Phys. Chem. Chem. Phys. 17, 30772-30774 (2015) DOI: 10.1039/C5CP90134K

K. Świderek, I. Tuñón, V. Moliner, J. Bertran "Computational strategies for the design of new enzymatic functions." Arch. Biochem. Biophys., 582, 68–79 (2015) DOI: 10.1016/j.abb.2015.03.013

V. Moliner  "Special issue in computational modeling on biological systems" Arch. Biochem. Biophys., 582, 1–2 (2015) DOI: 10.1016/j.abb.2015.07.013

K. Świderek, I. Tuñón, V. Moliner, J. Bertran "Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalysed by HG3.17" 
ACS Catalysis 5, 2587-2595, (2015) DOI: 10.1021/cs501904w

I.Viciano, P.Gonzalez-Navarrete, J.Andrés, S. Martí "Joint use of bonding evolution theory and QM/MM hybrid method for understanding the hydrogen abstraction mechanism via cytochrome P450 aromatase" J. Chem. Theory Comput., 11, 1470–1480 (2015) DOI:10.1021/ct501030q

C. Meliá, S. Ferrer, V. Moliner, J. Bertran "Theoretical studies of the hydrolysis of antibiotics catalyzed by a metallo-β-lactamase." Arch. Biochem. Biophys., 582, 116–126, (2015) DOI:10.1016/j.abb.2015.01.013

K. Świderek, I. Tuñón, S. Martí, V. Moliner "Protein Conformational Landscapes and Catalysis. Influence of active site conformations in the reaction catalyzed by L-Lactate Dehydrogenase." ACS Catalysis, 5, 1172-1185, (2015) DOI: 10.1021/cs501704f

A. Krzeminska, P. Paneth, V.Moliner, K. Świderek "Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT" 
J. Phys. Chem. B 119, 917-927, (2015) DOI: 10.1021/jp506119h 

-2014-

L. Y. P. Luk, J. J. Ruiz-Pernia, W. M. Dawson, E. J. Loveridge, I. Tuñón, V. Moliner, R. K. Allemann "Protein isotope effects in dihydrofolate reductase from Geo-bacillus stearothermophilus show entropic-enthalpic com-pensatory effects on the rate constant" J. Am. Chem. Soc. 136, 17317-17323, (2014)  DOI:10.1021/ja5102536

N. Gillet, B. Lévy, V. Moliner, I. Demachy, A. de la Lande "Electron and hydrogen atom transfers in the hydride carrier protein EmoB"  J. Chem. Theory Comput. 10, 5036–5046, (2014) DOI: 10.1021/ct500173y

K. Arafet, S. Ferrer, S. Martí, V. Moliner "QM/MM studies of mechanism of falcipain 2 inhibition by the epoxysuccinate E64." Biochemistry, 53, 3336-3346, (2014)
DOI: 10.1021/bi500060h

K. Świderek, J. J. Ruiz-Pernia, V. Moliner, I. Tuñón "Heavy enzymes — experimental and computational insights in enzyme dynamics" Curr. Opin. Chem. Biol., 21, 11-18, (2014) DOI: 10.1016/j.cbpa.2014.03.005

K. Świderek, S. Martí, V.Moliner "Theoretical study of primary reaction of Pseudozyma antarctica lipase B as the starting point to understand its promiscuity" 
ACS Catalysis, 4, 426–434, (2014) DOI: 10.1021/cs401047k 

K. Świderek, I. Tuñon, V. Moliner "Predicting enzymatic reactivity: from theory to design" WIREs Comput. Mol. Sci. 4, 407-421, (2014) DOI: 10.1002/wcms.1173

-2013-

J. J. Ruiz-Pernia, L. Y. P. Luk, R. García-Meseguer, S. Martí, E. J. Loveridge, I. Tuñón, V. Moliner,  R.K. Allemann "Increased Dynamic Effects in a Catalytically Compromised Variant of Escherichia coli Dihydrofolate Reductase" J. Am. Chem. Soc., 135, 18689–18696, (2013) DOI: 10.1021/ja410519h

C. Meliá, S. Ferrer, J. Řezáč, O. Parisel, O. Reinaud, V. Moliner, A. de la Lande "Investigation of the Hydroxylation Mechanism of Noncoupled Copper Oxygenases by Ab Initio Molecular Dynamics Simulations" Chem. Eur. J. 19, 17328-17337 (2013)  DOI: 10.1002/chem.201301000

N. de Farias Silva, J. Lameira, C. Nahum Alves, S. Martí "Computational study of the mechanism of half-reactions in class 1A dihydroorotate dehydrogenase from Trypanosoma cruzi" Phys. Chem. Chem. Phys. 15, 18863-18871, (2013)

Louis Y. P. Luk, J. Javier Ruiz-Pernía, William M. Dawson, Maite Roca, E. Joel Loveridge, David R. Glowacki,Jeremy N. Harvey, Adrian J. Mulholland, Iñaki Tuñón, Vicent Moliner, and Rudolf K. Allemann "Unraveling the role of protein dynamics in dihydrofolate reductase catalysis" Proc. Nat. Acad. Sci. USA. 110, 16344-16349 (2013)

K. Świderek, I. Tuñón, S. Martí, V. Moliner, J. Bertrán "Role of solvent on non-enzymatic peptide bond formation mechanism and Kinetic Isotope Effects" 
J. Am. Chem. Soc. 135, 8708-8719 (2013)

R. García-Meseguer, S. Martí, J. J. Ruiz-Pernía, V. Moliner, I. Tuñón "Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates" Nature Chemistry 5, 566–571 (2013)

Z. Wang; S. Ferrer; V. Moliner, A. Kohen "QM/MM Calculations Suggest a Novel Intermediate Following the Proton Abstraction Catalyzed by Thymidylate Synthase." Biochemistry 52, 2348-2358 (2013)

I. Viciano, S. Berski, S. Martí, J. Andrés "New insight into the electronic structure of iron(IV)-oxo porphyrin compound I. A quantum chemical topological analysis."
 J. Comput. Chem. 34, 780–789 (2013)

M. Reis, C.N. Alves, J. Lameira, I. Tuñón, S. Marti, V. Moliner "The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach" Phys. Chem. Chem. Phys. 15, 3772-3785 (2013)

-2012-

K. Świderek, A. Pabis, V. Moliner "A theoretical study of carbon-carbon bond formation by a Michael-type addition" Org. Bio. Chem. 10, 5598-5605 (2012)

K. Świderek, S. Martí, V. Moliner "Theoretical studies of HIV-1 reverse transcriptase inhibition" Phys. Chem. Chem. Phys. 14, 12614-12624 (2012)

NAN de Alencar, PRM Sousa, JRA Silva, J. Lameira, CN Alves, S. Marti, V. Moliner "Computational Analysis of Human OGA Structure in Complex with PUGNAc and NAG-Thiazoline Derivatives" J. Chem. Inf. Model. 52, 2775-2783 (2012)

J. J. Ruiz-Pernía, S. Martí, V. Moliner, I. Tuñón "A Novel Strategy to Study Electrostatic Effects in Chemical Reactions. Differences between the Role of Solvent and the Active Site of Chalcone Isomerase in a Michael Addition" J. Chem. Theory Comput. 8, 1532-1535 (2012)

M. Roca, J. Aranda, V. Moliner, I. Tuñón "Modeling Methods for Studying post-translational and transcriptional Modifying Enzymes" Curr. Op. Chem. Biol. 16, 465-471 (2012)

K. Świderek, I. Tuñón, S. Martí, V. Moliner, J. Bertrán "Do Zwitterionic Species Exist in the non-enzymatic Peptide Bond Formation?" Chem. Commun. 48, 11253-11255 (2012)

V. López-Canut, J. Javier Ruiz-Pernía, R. Castillo, V. Moliner, I. Tuñón "Hydrolysis of Phosphotriesteres: A Theoretical Analysis of the Enzymatic and Solution Mechanisms." Chemistry Eur. J. 18, 9612-9621 (2012)

S. Ferrer, S. Martí, J. Andrés, V. Moliner, I. Tuñón and J. Bertrán "Understanding the Different Activities of Highly Promiscuous MbtI by Computational Methods." 
Phys. Chem. Chem. Phys. 14, 3482–3489 (2012)

C. Melia, S. Ferrer, V. Moliner, I. Tuñón and J. Bertrán "A Computational Study on Hydrolysis of Cefotaxime (CEF). The Reaction Mechanism." J. Comput. Chem. 33, 1948-1959 (2012)

-2011-

S. Martí, V. Moliner, J. Andrés, M. Roca, V-López-Canut, E. Silla, I. Tuñón and J. Bertrán "Diseño computacional de catalizadores biológicos." An. Quim. 107, 144-153 (2011)

J.I. Mujika, X. Lopez, E. Rezabal, R. Castillo, S. Marti, V. Moliner, J.M. Ugalde "A QM/MM study of the complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH" J. Inor. Biochem. 105, 1446-1456 (2011)

V. Moliner "Eppur si muove" (yet it moves) Proc. Nat. Acad. Sci. USA. 108, 15013-15014 (2011)

N. Kanaan, S. Ferrer, M. García-Viloca, A. Kohen, S. Martí and V. Moliner "Theoretical Study of the Temperature Dependence of Kinetic Isotope Effects in Thymidylate Synthase." J. Am. Chem. Soc. 133, 6692–6702 (2011)

V. López-Canut, M. Roca, J. Bertrán, V. Moliner, I. Tuñón "Promiscuity in Alkaline Phosphatase Superfamily. Unraveling Evolution through Molecular Simulations." 
J. Am. Chem. Soc. 133, 12050–12062 (2011)

S. Ferrer, S. Martí, V. Moliner, I. Tuñón, J. Bertrán "Molecular Mechanism of promiscuous MbtI. Improving the Secondary Activity by a Computational Design." Theor. Chem. Acc. 128, 601-607 (2011)

J. Lameira, C. N. Alves, V. Moliner, S. Martí, I. Tuñón "Enzyme Molecular Mechanism as a Starting Point to Design New Inhibitors: A Theoretical Study of O-GlcNAcase" 
J. Phys. Chem. B 115, 6764-6775 (2011)

S. Martí, V. Moliner, I. Tuñón "Isochorismate Pyruvate Lyase Mechanism From High Accuracy Kinetic Isotope Effects calculations" Chem. Commun.  (2011)

N. Kanaan, S. Ferrer, M. García-Viloca, S. Martí, V. Moliner and A. Kohen "Temperature Dependence of Kinetic Isotope Effects in Thymidylate Synthase. A Theoretical Study" J. Am. Chem. Soc. 133, 6692-6702 (2011)