Subject teachers list
VILLÀ FREIXA, Jordi
Departament
Department of Basic AreasTeacher profile
Professor Catedràtic
Departament de Ciències Bàsiques. Universitat Internacional de Catalunya
Vicerector de Recerca, Innovació i Transferència de Coneixement 2019
Academic curriculum
- Química. Universitat Autònoma de Barcelona
Research interests
Reactivitat Enzimàtica; Modelatge Molecular; Bioquímica Computacional; Càlculs d'energia Lliure; Interacció de proteïnes
Relevant publications
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.
Projects and research
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
