Subject teachers list
VILLÀ FREIXA, Jordi
Departament
Departament de Ciències Bàsiques de Ciències de la SalutPerfil professor
Professor Catedràtic
Departament de Ciències Bàsiques. Universitat Internacional de Catalunya
Vicerector de Recerca, Innovació i Transferència de Coneixement 2019
Formació acadèmica
- Química. Universitat Autònoma de Barcelona
Interessos en recerca
Reactivitat Enzimàtica; Modelatge Molecular; Bioquímica Computacional; Càlculs d'energia Lliure; Interacció de proteïnes
Publicacions rellevants
Articles
- Agulló, L.; Buch, I.; Gutiérrez-de-Teran, H.; García-Dorado, D.; Villà-Freixa, J., (2016), "Computational exploration of the binding mode of heme‐dependent stimulators into the active catalytic domain of soluble guanylate cyclase", Proteins: structure, function, and bioinformatics, vol.84, No.10, pp. 1534-1548, ISSN: 1097-0134.
- Mulero, M.C.; Ferres-Marco, D.; Islam, A.; Margalef, P.; Pecoraro, M.; Toll, A.; Drechsel, N.; Charneco, C.; Davis, S.; Bellora, N.; Gallardo, F.; López-Arribillaga, E.; Asensio-Juan, E.; Rodilla, V.; González, J.; Iglesias, M.; Shih, V.; Albà, M.M.; di Croce, L.; Hoffmann, A.; Miyamoto, S.; Villà-Freixa, J.; López-Bigas, N.; Keyes, W.M.; Domínguez, M.; Bigas, A.; Espinosa, L., (2013), "Chromatin-bound IκBα regulates a subset of polycomb target genes in differentiation and cancer", Cancer cell, vol.24, No.2, pp. 151-166, ISSN: 1535-6108.
Articles
- Molinos-Albert, L.M.; Bilbao, E.; Agulló, L.; Marfil, S.; García, E.; Rodríguez de la Concepción, M.L.; Izquierdo-Useros, N.; Vilaplana, C.; Nieto-Garai, J.A.; Contreras, F.X.; Floor, M.; Cardona, P.J.; Martínez-Picado, J.; Clotet, B.; Villà-Freixa, J.; Lorizate, M.; Carrillo, J.; Blanco, J., (2017), "Proteoliposomal formulations of an HIV-1 gp41-based miniprotein elicit a lipid-dependent immunodominant response overlapping the 2F5 binding motif", Scientific Reports, vol.7, pp. 40800, ISSN: 2045-2322.
- Agulló, L.; Buch, I.; Gutiérrez-de-Teran, H.; García-Dorado, D.; Villà-Freixa, J., (2016), "Computational exploration of the binding mode of heme‐dependent stimulators into the active catalytic domain of soluble guanylate cyclase", Proteins: structure, function, and bioinformatics, vol.84, No.10, pp. 1534-1548, ISSN: 1097-0134.
- Pérez-Santiago, J.; Ouchi, D.; Urrea, V.; Carrillo, J.; Cabrera, C.; Villà-Freixa, J.; Puig, J.; Paredes, R.; Negredo, E.; Clotet, B.; Massanella, M.; Blanco, J., (2016), "Antiretroviral therapy suppressed participants with low CD4+ T-cell counts segregate according to opposite immunological phenotypes", AIDS, vol.30, No.15, pp. 2275-2287, ISSN: 0269-9370.
- Drechsel, N.; Fennell, C.J.; Dill, K.A.; Villà-Freixa, J., (2014), "TRIFORCE: Tessellated semianalytical solvent exposed surface areas and derivatives", Journal of chemical theory and computation, vol.10, No.9, pp. 4121-4132, ISSN: 1549-9618.
- Tajes, M.; Eraso-Pichot, A.; Rubio-Moscardó, F.; Guivernau, B.; Ramos-Fernández, E.; Bosch-Morató, M.; Guix, F. X.; Clarimón, J.; Miscione, G.; Boada, M.; Gil-Gómez, G.; Suzuki, T.; Molina, H.; Villà-Freixa, J.; Rubén, V.; Muñoz, F., (2014), "Methylglyoxal produced by amyloid-β peptide-induced nitrotyrosination of triosephosphate isomerase triggers neuronal death in Alzheimer's disease", Journal of alzheimers disease, vol.41, No.1, pp. 273-288, ISSN: 1387-2877.
- Mulero, M.C.; Ferres-Marco, D.; Islam, A.; Margalef, P.; Pecoraro, M.; Toll, A.; Drechsel, N.; Charneco, C.; Davis, S.; Bellora, N.; Gallardo, F.; López-Arribillaga, E.; Asensio-Juan, E.; Rodilla, V.; González, J.; Iglesias, M.; Shih, V.; Albà, M.M.; di Croce, L.; Hoffmann, A.; Miyamoto, S.; Villà-Freixa, J.; López-Bigas, N.; Keyes, W.M.; Domínguez, M.; Bigas, A.; Espinosa, L., (2013), "Chromatin-bound IκBα regulates a subset of polycomb target genes in differentiation and cancer", Cancer cell, vol.24, No.2, pp. 151-166, ISSN: 1535-6108.
- Margalef, P.; Fernández-Majada, V.; Villanueva, A.; Garcia-Carbonell, R.; Iglesias, M.; López, L.; Martínez-Iniesta, M.; Villà-Freixa, J.; Mulero, M.C.; Andreu, M.; Torres, F.; Mayo, M. W.; Bigas, A.; Espinosa, L., (2012), "A truncated form of IKKα is responsible for specific nuclear IKK activity in colorectal cancer", Cell Reports, vol.2, No.4, pp. 840-854, ISSN: 2211-1247.
- Dalton, J.; Kalid, O.; Schuchan, M.; Ben-Tal, N.; Villà-Freixa, J., (2012), "New model of cystic fibrosis transmembrane conductance regulator proposes active channel-like conformation", Journal of chemical information and modeling, vol.52, No.7, pp. 1842-1853, ISSN: 1549-9596.
- Maier, D.; Klaus, W.; Wolff, M.; Kalko, S. G.; Roca, J.; Marín de Mas, I.; Turan, N.; Cascante, M.; Falciani, F.; Hernández, M.; Villà-Freixa, J.; Losko, S., (2011), "Knowledge management for systems biology a general and visually driven framework applied to translational medicine", BMC systems biology, vol.5, pp. 38, ISSN: 1752-0509.
- Cooper, J.; Cervenansky, F.; de Fabritiis, G.; Fenner, J.; Friboulet, D.; Giorgino, T.; Manos, S.; Martelli, Y.; Villà-Freixa, J.; Zasada, S.; Lloyd, S.; McCormack, K.; Coveney, P., (2010), "The Virtual Physiological Human TOOLKIT", Philosophical transactions of the Royal Society A. Mathematical physical and engineering sciences, vol.368, No.1925, pp. 3925-3936, ISSN: 1364-503X.
- Rué, P.; Villà-Freixa, J.; Burrage, K., (2010), "Simulation methods with extended stability for stiff biochemical Kinetics", BMC systems biology, vol.4, No.1, pp. 110, ISSN: 1752-0509.
- Guix, F. X.; Ill-Raga, G.; Bravo, R.; Nakaya, T.; de Fabritiis, G.; Coma, M.; Miscione, G.; Villà-Freixa, J.; Suzuki, T.; Fernández-Busquets, X.; Valverde, M. A.; De Strooper, B.; Muñoz, F. J., (2009), "Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation", Brain, vol.132, No.5, pp. 1335-1345, ISSN: 0006-8950.
- de Fabritiis, G.; Coveney, P.; Villà-Freixa, J., (2008), "Energetics of K+ permeability through Gramicidin A by forward‐reverse steered molecular dynamics", Proteins: structure, function, and bioinformatics, vol.73, No.1, pp. 185-194, ISSN: 1097-0134.
- Johnston, M. A.; Fernández-Galván, I.; Villà-Freixa, J., (2005), "Framework‐based design of a new all‐purpose molecular simulation application: The Adun simulator", Journal of computational chemistry, vol.26, No.15, pp. 1647-1659, ISSN: 0192-8651.
- Centeno, N.B.; Villà-Freixa, J.; Oliva, B., (2003), "Teaching structural bioinformatics at the undergraduate level", Biochemistry and molecular biology education, vol.31, No.6, pp. 386-391, ISSN: 1470-8175.
- Barbany, M.; Gutiérrez-de-Teran, H.; Sanz, F.; Villà-Freixa, J.; Warshel, A., (2003), "On the generation of catalytic antibodies by transition state analogues", Chembiochem, vol.4, No.4, pp. 277-285, ISSN: 1439-4227.
- Truhlar, D. G.; Gao, J.; Alhambra, C.; Garcia-Viloca, M.; Corchado, J.; Sánchez, M.; Villà-Freixa, J., (2002), "The incorporation of quantum effects in enzyme kinetics modeling", Accounts of chemical research, vol.35, No.6, pp. 341-349, ISSN: 0001-4842.
- Burykin, A.; Schutz, C. N.; Villà-Freixa, J.; Warshel, A., (2002), "Simulations of ion current in realistic models of ion channels: the KcsA potassium channel", Proteins: structure, function, and bioinformatics, vol.47, No.3, pp. 265-280, ISSN: 1097-0134.
- Shurki, A.; Strajbl, M.; Villà-Freixa, J.; Warshel, A., (2002), "How much do enzymes really gain by restraining their reacting fragments?", Journal of the American Chemical Society, vol.124, No.15, pp. 4097-4107, ISSN: 0002-7863.
- Villà-Freixa, J.; Warshel, A., (2001), "Energetics and dynamics of enzymatic reactions", Journal of physical chemistry B, vol.105, No.33, pp. 7887-7907, ISSN: 1520-6106.
- Warshel, A.; Florian, J.; Strajbl, M.; Villà-Freixa, J., (2001), "Circe effect versus enzyme preorganization: What can be learned from the structure of the most proficient enzyme?", Chembiochem, vol.2, No.2, pp. 109-111, ISSN: 1439-4227.
- Warshel, A.; Strajbl, M.; Villà-Freixa, J.; Florian, J., (2000), "Remarkable rate enhancement of orotidine 5 '-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization", Biochemistry, vol.39, No.48, pp. 14728-14738, ISSN: 0006-2960.
- Villà-Freixa, J.; Strajbl, M.; Glennon, T.M.; Sham, Y.Y.; Chu, Z.T.; Warshel, A., (2000), "How important are entropic contributions to enzyme catalysis?", Proceedings of the National Academy of Sciences of the United States of America, vol.97, No.22, pp. 11899-11904, ISSN: 0027-8424.
- Glennon, T.M.; Villà-Freixa, J.; Warshel, A., (2000), "How does GAP catalyze the GTPase reaction of Ras?: A computer simulation study", Biochemistry, vol.39, No.32, pp. 9641-9651, ISSN: 0006-2960.
- Strajbl, M.; Sham, Y.Y.; Villà-Freixa, J.; Chu, Z.T.; Warshel, A., (2000), "Calculations of activation entropies of chemical reactions in solution", Journal of physical chemistry B, vol.104, No.18, pp. 4578-4584, ISSN: 1520-6106.
- Kim, Y.; Corchado, J.C.; Villà-Freixa, J.; Xing, J.; Truhlar, D.G., (2000), "Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions", Journal of chemical physics, vol.112, No.6, pp. 2718-2735, ISSN: 0021-9606.
- Villà-Freixa, J.; Bentzien, J.; González-Lafont, À.; Lluch, J.; Bertrán, J.; Warshel, A., (2000), "Effective way of modeling chemical catalysis: Empirical valence bond picture of role of solvent and catalyst in alkylation reactions", Journal of computational chemistry, vol.21, No.8, pp. 607-625, ISSN: 0192-8651.
- Villà-Freixa, J.; Corchado, J.; González-Lafont, À.; Lluch, J.; Truhlar, D. G., (1999), "Variational transition-state theory with optimized orientation of the dividing surface and semiclassical tunneling calculations for deuterium and muonium kinetic isotope effects in the free radical association reaction H+C2H4 -> C2H5", Journal of physical chemistry A, vol.103, No.26, pp. 5061-5074, ISSN: 1089-5639.
- Alhambra, C.; Gao, J.; Corchado, J.; Villà-Freixa, J.; Truhlar, D. G., (1999), "Quantum mechanical dynamical effects in an enzyme-catalyzed proton transfer reaction", Journal of the American Chemical Society, vol.121, No.10, pp. 2253-2258, ISSN: 0002-7863.
- Villà-Freixa, J.; Corchado, J.; González-Lafont, À.; Lluch, J.; Truhlar, D. G., (1998), "Explanation of deuterium and muonium kinetic isotope effects for hydrogen atom addition to an olefin", Journal of the American Chemical Society, vol.120, No.46, pp. 12141-12142, ISSN: 0002-7863.
- Villà-Freixa, J.; González-Lafont, À.; Lluch, J.; Truhlar, D. G., (1998), "Entropic effects on the dynamical bottleneck location and tunneling contributions for C2H4+H -> C2H5: Variable scaling of external correlation energy for association reactions", Journal of the American Chemical Society, vol.120, No.22, pp. 5559-5567, ISSN: 0002-7863.
- González-Lafont, À.; Villà-Freixa, J.; Lluch, J.; Bertrán, J.; Steckler, R.; Truhlar, D. G., (1998), "Variational transition state theory and tunneling calculations with reorientation of the generalized transition states for methyl cation transfer", Journal of physical chemistry A, vol.102, No.19, pp. 3420-3428, ISSN: 1089-5639.
- Villà-Freixa, J.; González-Lafont, À.; Lluch, J. M.; Corchado, J.; Espinosa-García, J., (1997), "Understanding the activation energy trends for the C2H4 +OH -> C2H4OH reaction by using canonical variational transition state theory", Journal of chemical physics, vol.107, No.18, pp. 7266-7274, ISSN: 0021-9606.
- Villà-Freixa, J.; Truhlar, D. G., (1997), "Variational transition state theory without the minimum-energy path", Theoretical chemistry accounts, vol.97, No.1-4, pp. 317-323, ISSN: 1432-881X.
Projectes de recerca
Exploring peptide/MHC dissociation landscapes using Hierarchical Natural Move Monte Carlo
IP: Villà-Freixa, J.
MINE - MINECO. Ministerio de Economía y Competitividad
01/09/2019 - 31/12/2021
