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Computational biochemistry and soft matter

Using the battery of available computational methods, from electronic structure based methods to classical simulations, we focus on systems of biological interest. In particular we investigate the structure and reactivity of proteins and enzymes, drug design, processes in cellular membranes, enzymatic reactions in crowded media and soft nanoparticles in solution.


The most relevant highlights in this topic are:


Identification of Potential Small Molecule Binding Pockets in p38α MAP kinase

P. Gomez-Gutierrez, J. Rubio-Martinez, J. J. Perez.
J. Chem. Inf. Model., 57 (2017) 2566.

Bioengineering a Single-Protein Junction

M. P. Ruiz, A. C. Aragonès, N. Camarero, J. G. Vilhena, M. Ortega, L. A. Zotti, R. Pérez, J. C. Cuevas, P. Gorostiza, I. Díez-Pérez.
J. Am. Chem. Soc.,139 (2017) 15337.

B-DNA model systems in non-terran bio-solvents: implications for structure, stability and replication

T. A. Hamlin, J. Poater, C. Fonseca Guerra, F. M. Bickelhaupt.
Phys. Chem. Chem. Phys., 19 (2017) 16969.

A Front-Face ‘SNi synthase’ engineered from a retaining ‘double-SN2’ hydrolase

J. Iglesias-Fernández, S. M. Hancock, S. S. Lee, M. Khan, J. Kirkpatrick, N. J. Oldham, K. McAuley, A. Fordham-Skelton, C. Rovira, B. G. Davis.
Nat. Chem. Biol., 13 (2017) 874.

Ionization and Conformational Equilibria of Citric Acid: Delocalized Proton Binding in Solution

S. Madurga, M. Nedyalkova, F. Mas, J. L. Garcés.
J. Phys. Chem. A, 121 (2017) 5894.

Effects of Fullerene on lipid bilayers displaying different liquid ordering: a coarsegrained molecular dynamics study

J. Sastre, I. Mannelli, R. Reigada.
Biochim. Biophys. Acta - General Subjects, 1861 (2017) 2872.


A trapped covalent intermediate of a glycoside hydrolase on the pathway to transglycosylation. Insights from experiments and QM/MM simulations

L. Raich, V. Borodkin, W. Fang, J. Castro-López, D. van Aalten, R. Hurtado-Guerrero, C. Rovira.
J. Am. Chem. Soc., 138 (2016) 3325.

Dealing with long-range interactions in the determination of polyelectrolyte ionization properties. Extension of the transfer matrix formalism to the full range of ionic strengths

J. L. Garcés, S. Madurga, C. Rey-Castro, F. Mas.
J. Polym. Sci. Part B. Polym. Phys., doi: 10.1002/polb.24269.

Functionalized surfaces with tailored wettability determine influenza A infectivity

I. Mannelli, R. Reigada, I. Suárez, D. Janner, A. Carrilero, P. Mazumder, F. Sagués, V. Pruneri, M. Lakadamyali.

ACS Applied Materials and Interfaces, 8 (2016) 15058.

Assessment of the sampling performance of multiple-copy dynamics versus a unique trajectory

J. J. Pérez, M. S. Tomas, J. Rubio-Martínez.

J. Chem. Inf. Model., 56 (2016) 1950.



Absence of a Stable Secondary Structure Is Not a Limitation for Photoswitchable Inhibitors of βArrestin/ βAdaptin 2 ProteinProtein Interaction

A. Martín-Quirós, L. Nevola, K. Eckelt, S. Madurga, P. Gorostiza, E. Giralt.

Chemistry & Biology, 22 (2015) 31.

Insight into the Binding of DFG-out Allosteric Inhibitors to B-Raf Kinase Using Molecular Dynamics and Free Energy Calculations

L. Coronel, JM, Granadino-Roldán, M. Pinto, MS. Tomas, MD. Pujol, J. Rubio-Martinez.

Current Computer-Aided Drug Design. 11 (2015) 124.

Reaction mechanisms in carbohydrate-active enzymes: glycoside hydrolases and glycosyltransferases. Insights from ab initio QM/MM dynamic simulations

A. Ardèvol, C. Rovira
J. Am. Chem. Soc., 137 (2015) 7528 (Perspective). Editor’s choice & JACS Spotlight.

Chloroform alters interleaflet coupling in lipid bilayers: an entropic mechanism

R. Reigada, F. Sagués.
J. R. Soc. Interface, 12 (2015) 20150197.


Coupling of conformational and ionizatin equilibria in linear poly(ethylenimine): a study based on site binding/rotational isomeric state (SBRIS) model

J.L. Garcés, S. Madurga, M. Borkovec

Phys. Chem. Chem. Phys., 16 (2014) 4626.

Theoretical study of the free energy surface and kinetics of the hepatitis C virus NS3/NS4A serine protease reaction with the NS5A/5B substrate. Does the generally accepted tetrahedral intermediate really exist?

J. A. Martínez-González, M. González, L. Masgrau, R. Martínez

ACS Catal. in press (

Design of an interface peptide as new inhibitor of humanglucose-6-phosphate dehydrogenase

C. Obiol-Pardo, G. Alcarraz-Vizánb, S. Díaz-Moralli, M. Cascante, J. Rubio-Martinez

Journal of Molecular Graphics and Modelling, 49 (2014) 110.

An ionizable triptophane residue imparts catalase activity to a peroxidase core

P. C. Loewen, X. Carpena, P. Vidossich, I. Fita, C. Rovira

J. Am. Chem. Soc., 136 (2014) 7249. JACS Spotlight.

Effects of Dimethyl Sulfoxide on Lipid Membrane Electroporation

M.L. Fernández, R. Reigada

J. Phys. Chem. B, 118 (2014) 9306.



Effect of crowding by Dextrans in enzymatic reactions

I. Pastor, C. Balcells, L. Pitulice, E. Vilaseca, S. Madurga, A. Isvoran, M. Cascante, F.

Biophysical Chemistry, 185 (2013) 8

Structural analysis of the inhibition of APRIL by TACI and BCMA through molecular dynamics simulations

M. González-Mendióroz, A-B. Álvarez-Vázquez, J. Rubio-Martinez

J. Mol. Graph Model., 39 (2013) 13

Formation of a covalent glycosyl-enzyme species in a retaining glycosyltransferase

V. Rojas-Cervellera, A. Ardèvol, M. Boero, A. Planas, C. Rovira.

Chem. Eur. J. 42 (2013) 14018.

Negative feedback self-regulation contributes to robust and high-fidelity transmembrane signall transduction

M.A. Serrano, M. Jurado, R. Reigada.

J. R. Soc. Interface, 10 (2013) 20130581.


 Molecular dynamics simulation of the spherical electrical double layer of a soft nanoparticle. Effect of the surface and counterion valence.

M. Nedyalkova, S. Madurga, S. Pisov, I. Pastor, E. Vilaseca, F. Mas.
J. Chem. Phys., 137 (2012) 174701.


Molecular Determinants of Bim(BH3) Peptide Binding to Pro-Survival Proteins.

L. Delgado-Soler, M. Pinto, K. Tanaka-Gil , J. Rubio-Martinez.
J. Chem. Inf. Model., 52 (2012) 2107.


The reaction coordinate of a bacterial GH47 α-mannosidase: a combined quantum mechanical and structural approach.

A. J. Thompson, J. Dabin, J. Iglesias-Fernández, A. Ardèvol, Z. Dinev, S. J. Williams, O. Bande, A. Siriwardena, C. Moreland, T.-C. Hu, D. K. Smith, H. J. Gilbert, C. Rovira*, G. J. Davies*.
Angew. Chem. Int. Ed. 51 (2012) 10997-11001. Selected as Very Important Paper (VIP, top 5% of the journal). Inside back cover.


Effects of Dymethyl Sulfoxide in Cholesterol-Containing Lipid Membranes: A Comparative Study of Exeriments In Silico and with Cells.

M-A. de Ménorval, LL.M. Mir, M.L. Fernández, R. Reigada.
PLoS One, 7 (2012) e41733.


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