Molecular and Industrial Biotechnology group. GBMI

Juan Jesús Pérez contributions

Scientific contributions

Peer reviewed articles

  • Ruiz, M.; Roset, L.; Demey, H.; Castro, S.; Sastre, A.M.; Perez, J. J. Equilibrium and dynamic studies for adsorption of boron on calcium alginate gel beads using principal component analysis (PCA) and partial least squares (PLS). Mat.-wiss.
  • u.Werkstofftech Perez, J.J. Amygdalin analogs for the tratment of psoriasis. Fut. Med. Chem., 2013, 5, 799–808
  • Lupala, C.L.; Gomez-Gutierrez, P.; Perez, J.J. Molecular determinants of the bacterial resistance to fluoroquinolones: A computational study. Curr. Comp.-Aided Drug Des., in press
  • Torrent-Burgués, J.; Vocanson, F.; Perez, J.J. Synthesis, Langmuir and Langmuir-Blodgett films of a calix[7]arene ethyl ester. AFM characterization, subphase influence and molecular modelling. Coll. Surf. A, 2012, 401, 137-147
  • Martinez-Archundia, M.; Cordomi, A.; Garriga, P.; Perez, J.J. Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site. J. Biomed. Biotech., 2012, 1-12, Article ID 789741.
  • Toledo, D., Ramon, E., Aguila, M., Cordomi, A., Perez, J.J., Mendes, H.F., Cheetham, M.E., Garriga, P. Molecular Mechanisms of Disease for Mutations at Gly-90 in Rhodopsin. J. Biol. Chem. 2011, 286, 39993-40001
  • Jaillet, L.; Corcho, F.J.; Perez, J.J.; Cortés, J. A randomized tree construction algorithm to explore energy landscapes. J. Comp. Chem., 2011,32, 3464-3474
  • Singh, P.; Sharma, P.; Bisetty, K.; Corcho, F.; Perez. J.J. Comparative structural studies of T-20 analogues using molecular dynamics., Comp. Theor. Chem., 2011, 971, 1-7
  • Pinto, M.; Orzaez, M. M.; Delgado, L.; Perez-Paya, E.; Perez, J.J.; Rubio-Martinez, J. Rational design of a new class of BH3-mimetics as inhibitors of the Bcl-xL protein. J. Chem. Inf. Compt. Sci., 2011, 51, 1249-1258
  • Rodriguez, A.; Mokoema,. P.; Corcho, F.J.; Bisetty, K.; Perez, J. J. Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent. J. Phys. Chem. B, 2011, 115, 1440–1449
  • Perez, J.J. Is the folding topology of a protein related to its amino acid occurrence? J. Biomol. Struct. Dyn., 2011, 28, 657-659.
  • Sharma, P.; Singh, P; Bisetty, K.; Rodriguez, A. ; Perez, J.J. Conformational space search of Neuromedin C using replica exchange molecular dynamics and molecular dynamics. J. Pept. Sci, 2011, 17, 174–183
  • Sharma, P.; Singh, P.; Bisetty, K.; Pérez, J. J. A computational study of Neuromedin B. Comp. Theor. Chem. 2011, 971, 1-7.
  • Roset, L.; Perez, J.J. Computation of Molecular Polarizabilities using the Functional Density Theory through the Analysis of molecular polarization maps. J. Comp. Meth. Sci. Eng., 2011, 10, 521-529
  • Sharma, P.; Singh, P.; Bisetty, K.; Corcho, F. J.; Perez, J.J. Conformational profile of bombesin assessed using different computational protocols. J. Mol Graph. Model., 2010, 29, 581–590
  • Sigh, P.; Sarma, P.; Perez, J.J.; Bisetty, K. Molecular Dynamics Simulations of Ac-3Aib-Cage-3Aib-NHMe. Molec. Simul., 2010, 36,1035–1044
  • Perez, J.J.; Corcho, F.J.; Rubio-Martinez, J. Design of Peptidomimetics. In “Burger’s Medicinal Chemistry, Drug discovery, and Development”. 7th Edition. Abraham, D.J. and Rotella, D.P. (Eds.), Wiley and Sons, New York, 2010.
  • Cordomi, A.; Prades, J.; Frau, J.; Voegler, O.; Funari, S.; Perez, J.J.; Escriba, P. V.; Barcelo, F. Interactions of fatty acids with phosphatidylethanolamine membranes: X-ray diffraction and molecular dynamics studies. J. Lipid Res., 2010, 51, 1113-1124.
  • Mairal, T.; Nieto, J.; Pinto, M.; Almeida, M.R.; Gales, L.; Ballesteros, A.; Barluenga, J.; Perez, J. J.; Vazquez, J.T.; Centeno, N. B.; Saraiva, M.J.; Damas, A.M.; Planas, A.; Arsequell, G.; Valencia, G. Iodine Atoms: A New Molecular Feature for the Design of Potent Transthyretin Fibrillogenesis Inhibitors. PLOS ONE, 2009, 4, e4124.
  • Cordomi, A; Perez, JJ. Structural Rearrangements of Rhodopsin Subunits in a Dimer Complex: a Molecular Dynamics Simulation Study. J. Biomol. Struct. Dyn., 2009, 27, 127-147.
  • Gomez-Gutierrez, P.; Perez, J.J. Key Interactions responsible of molecular recognition process between MKK-derived D-site peptides and MAPKs. Drugs Future, 2009, 34, 171.
  • Pinto, M.; Orzaez, M.D.; Perez-Paya, E.; Perez, J.J.; Rubio-Martinez, J. Structure-based discovery of new small-molecule inhibitors of the antiapoptotic protein bcl-xL. Drugs Future, 2009, 34, 136.
  • Cordomi, A.; Edholm, O.; Perez, J.J. Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers. J. Chem. Theor. Comput., 2009, 5, 2125-2134.
  • Roset, L.; Rubio-Martinez, J.; Perez, J.J. Analysis of the basis set and correlation effects on the computation of molecular polarizabilities using molecular polarization maps. Theor. Chem. Acc., 2009, 123, 113-118.
  • Corcho, F.J.; Mokoena, P.; Bisetty, K.; Perez, J.J. Molecular Dynamics (MD) Simulations of VIP and PACAP27. Biopolymers, 2009, 91, 391-400.
  • Bisetty, K.; Perez, J.J. Conformational study of the pcu cage monopeptide: a key role of some force-field parameters. J. Phys. Chem. B, 2009, 113, 5234-5238.
  • Toledo, D.; Cordomi, A.; Proietti, M.G.; Benfatto, M.; del Valle, L. J. Perez, J.J. Garriga, P.; Sepulcre, F. Structural characterization of a zinc high-affinity binding site in rhodopsin. Photochem. Photobiol., 2009, 85, 479-484.
  • Rodriguez, A.; Canto, J.; Corcho, F.; Perez, J.J. Computational investigation of the conformational profile of the four stereomers of Ac-L-Pro-c(3)Phe-NHMe (c(3)Phe= 2,3-methanophenylalanine). Biopolymers, 2009, 92, 518-524.
  • Cordomi, A.; Ramon, E.; Garriga, P.; Perez, J.J. Molecular dynamics simulations of rhodopsin point mutants at the cytoplasmic side of helices 3 and 6. J. Biomol. Struct. Dyn., 2008, 25, 573-587.
  • Cordomi, A.; Edholm, O.; Perez, J.J. Effect of ions on a dipalmitoyl phosphatidylcholine bilayer. A molecular dynamics simulation study. J. Phys. Chem. B, 2008, 112, 1397-1408
  • Porta, J.M.; Ros, L.; Thomas, F.; Corcho, F., Canto, J; Perez, J.J. Erratum: Complete maps of molecular-loop conformational spaces (Journal of Computational Chemistry. 2007, 28, 2170). J. Comput. Chem., 2008, 29, 144-155.
  • Corcho, F.; Salvatella, X. ;Canto, J.; Giralt, E.; Perez, J.J. Structural Analysis of Substance P Using Molecular Dynamics and NMR Spectroscopy. J. Pept. Sci., 2007, 13, 728-741.
  • Porta, J.M.; Ros, L.; Thomas, F.; Corcho, F., Canto, J; Perez, J.J. Complete maps of molecular-loop conformational spaces. J. Comput. Chem., 2007, 28, 2170-2189.
  • Bisetty, K.; Kruger, H.; Perez, J.J. A molecular dynamics study of the pentacyclo-undecane (PCU) cage polypeptides of the type Ac-3Ala-Cage-3Ala-NHMe. Mol. Simul., 2007, 33, 1105-1108.
  • Cordomi, A.; Perez, J.J. Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers. J. Phys. Chem. B, 2007, 111, 7052-7063.
  • Ramon, E. Cordomi, A.; Bosch, L.; Zernii, E.Y.; Senin, I.I.; Manyosa, J.; Philippov, P.P.; Perez, J.J. Critical role of electrostatic interactions of amino acids at the cytoplasmic region of helices 3 and 6 in rhodopsin conformational properties and activation. J. Biol. Chem., 2007, 282, 14272-14282.
  • Sepulcre, F.; Cordomi, A.; Proietti M.G.; Perez, J.J.; Garcia, J.; Querol, E.; Padros, E. X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane. Proteins: Struct. Funct. Bioinf., 2007, 67, 360-374.
  • Cordomi, A.; Edholm, O.; Perez, J.J. Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. J. Comput. Chem., 2007, 28, 1017-1030.
  • Bosch, L.; Cordomi, A; Dominguez, M.; Toledo, D.; Morillo, M.; Perez, J.J.; Alvarez, R.; de Lera A.R.; Garriga, P. A methyl group at C7 of 11-cis-retinal allows chromophore formation but affects rhodopsin activation. Vision Res., 2006, 46, 4472-4481.
  • Bisetty, K. ; Corcho, F.J.; Canto, J.; Kruger, H.G.; Perez, J.J. A Molecular dynamics study of the pentacyclo-undecane cage amino acid tripeptide. J. Mol. Struct. (THEOCHEM), 2006, 770, 221-228.
  • Bisetty, K.; Corcho, F.J.; Canto, J.; Kruger, H.G.; Perez, J. J. Simulated annealing study of the pentacyclo-undecane cage amino acid tripeptides of the type (Ac-X-Y-Z-NHMe). J. Mol. Struct. (THEOCHEM), 2006, 759, 145-157.
  • Bisetty, K.; Corcho, F.J.; Canto, J.; Kruger, H.G.; Perez, J.J. A theoretical study of the pentacyclo-undecane cage peptides of the type (Ac-X-Y-NHMe). J. Pept. Sci., 2006, 12, 92-105.
  • Casanovas, J.; Jimenez, A.I.; Cativiela, C.; Perez, J.J.; Aleman, C. Conformational Analysis of a Cyclopropane Analogue of Phenylalanine with Two Geminal Phenyl Substituents. J. Phys. Chem. B, 2006, 110, 5762-5766.
  • Baroni, A.; Paoletti, I.; Greco, R.; Satriano, R.A.; Ruocco, E.; Tufano, M.A.; Perez, J.J. Imunodulatory effects of a set of amygdalin analogues on human keratinocyte cells. Exp. Dermatol., 2005, 14, 854-859.
  • Rodriguez, A.; Tomas, M.S.; Perez, J.J.; Rubio-Martinez, J. Assessment of the performance of cluster analysis grouping using pharmacophores as molecular descriptors. J. Mol. Struct. (THEOCHEM), 2005, 727, 81-87.
  • Perez, J.J. Managing molecular diversity. Chem. Soc. Rev., 2005, 34, 143-152.
  • Bisetty, K.; Gomez-Catalan, J.; Perez, J.J. Conformational analysis of small peptides of the type Ac-X-Me, where X=Gly,Ala,Aib and Cage. J. Mol. Struct. (THEOCHEM), 2005, 73, 127-137.
  • Araya, E. Rodriguez, A.; Rubio, J.; Spada, A.; Joglar, J.; Llebaria, A.; Lagunas, C.; Fernandez, A.G.; Spisani, S.; Perez, J.J. Synthesis and Evaluation of Diverse Analogs of Amygdalin as Potential Peptidomimetics of Peptide T. Bioorg. Med. Chem. Lett., 2005, 15, 1493-1496.
  • Aleman, C.; Jimenez, A.I.; Cativiela, C.; Perez, J.J.; Casanovas, J. Unusually high pyramidal geometry of the bicyclic amide nitrogen in a complex 7-azabicyclo[2.2.1]heptane derivative: theoretical analysis using a bottom-up strategy. J. Phys. Chem. B, 2005, 109, 11836-11841.
  • Corcho, F.; Cantó, J.; Perez, J.J. Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics. J. Comput. Chem., 2004, 25, 1937-1952.
  • Bisetty, K.; Gomez-Catalan, J.; Aleman, C.; Giralt, E.; Kruger, H.G.; Perez, J.J. Computational study of the conformational preferences of the (R)-8-amino-pentacyclo(5.4.0.0.0.0)undecane-8-carboxylic acid monopeptide. J. Pept. Sci., 2004, 10, 274-284.
  • Pinto, M.; Perez, J.J.; Rubio-Martinez, J. Molecular dynamics Study of peptide segments of the BH3 domain of the proapoptotic proteins Bak, Bax, Bid and Hrk bound to the Bcl-xL and Bcl-2 proteins. J. Comput.-Aided Mol. Design, 2004, 18, 13-22.
  • Casanovas, J.; Jimenez, A.I.; Cativiela, C.; Perez, J.J.; Aleman, C. N-Acetyl-N´-methylamide derivative of (2S,3S)-1-amino-2,3-diphenylcyclopropane carboxylic acid: Theoretical analysis of the conformational impact produced by the incorporation of the second phenyl group to the cyclopropane anlogue of phenylalanine. J. Org. Chem., 2003, 68, 7088-7091.
  • Cantó, J.; Isabel, H.; Alsina, M.A.; Perez, J.J. Analysis of the Differential Conformational Behavior of Two Antigens of the Hepatitis A Virus through Molecular Dynamics and Physicochemical Measurements. J. Phys. Chem. B, 2003, 107, 6603-6608.
  • Perez, J.J.; Corcho, F.; Llorens, O. Molecular modeling in the design of peptidomimetics and peptide surrogates. Curr. Med. Chem., 2002, 9, 2209-2229.
  • Llorens, O.; Perez, J.J.; Corcho, F. Investigation of structural and electronic biases in mutagenic compounds. Int. J. Quantum Chem., 2002, 88, 107-117.
  • Alemán, C.; Jimenez, A.I.; Cativiela, C.; Perez, J.J.; Casanovas, J. Influence of the phenyl side chain on the conformation of cyclopropane analogues of phenylalanine. J. Phys. Chem. B, 2002, 106, 11849-11858.
  • del Valle, L.J.; Escribano, C.; Perez, J.J.; Garriga, P. Calcium-induced decrease of the thermal stability and chaperone activity of alfa-crystallin. Biochim. Biophys. acta., 2002, 1601, 100-109.
  • Aleman, C.; Jimenez, A.I.; Cativiela, C.; Perez, J.J.; Casanovas, J. Influence of the phenyl side chain on the conformation of cyclopropane analogues of phenylalanine. J. Phys. Chem. B, 2002, 106, 11849-11858.
  • Cordomí, A.; Gomez-Catalan, J.; Jimenez, A.I.; Cativiela, C.; Perez, J.J. Study of the conformational profile of the norbornane analogues of phenylalanine. J. Pept. Sci., 2002, 8, 253-266.
  • Villacañas, O.; Perez, J.J.; Rubio-Martinez, J. Structural Analysis of the inhibition of Cdk4 and Cdk6 by p16 through molecular dynamics simulations. J. Biomol. Struct. Dyn., 2002, 20, 347-358.
  • Llorens, O.; Perez, J.J.; Palomer, A.; Mauleon, D. Differential binding mode of diverse cyclooxygenase inhibitors. J. Mol. Graph. Model., 2002, 20, 359-371.
  • Filizola, M; Perez, J.J. Assessment of the bioactive conformation of the vasoactive intestinal peptide by computational methods. Int. J. Quantum Chem., 2002, 88, 201-210
  • Carbonell, T. ; Masip, I.; Sanchez-Baeza, F.; Delgado, M.; Araya, E.; Llorens, O.; Corcho, F.; Perez, J.J.; Perez-Paya; E.; Messeguer, A. Identification of selective inhibitors of acetylcholinesterase from a combinatorial library of 2,5-piperazinediones. Mol. Diver., 2002, 5, 435-446.
  • Gomez-Catalan, J.; Jimenez, A.; Cativiela, C.; Perez, J.J. Study of the Conformational Profile of the cyclohexane analogs of L-phenylalanine. J. Pept. Res., 2001, 57, 435-446.
  • Perez, J.J. Aplicació de mètodes molecular computacionals en el disseny de molècules bioactives. Butlletí de les societats catalanes de física, química, matemàtiques i tecnologia, 2001, 2, 56-62.
  • Llorens, J.; Perez, J.J.; Villar, H. Toward the design of chemical libraries for mass screening biased against mutagenic compounds. J. Med. Chem., 2001, 44, 2793-2804.
  • Carbonell, T. ; Masip, I.; Sanchez-Baeza, F.; Delgado, M.; Araya, E.; Llorens, O.; Corcho, F.; Perez, J.J.; Perez-Paya; E.; Messeguer, A. Identification of selective inhibitors of acetylcholinesterase from a combinatorial library of 2,5-piperazinediones. Mol. Diver., 2000, 5, 131-143.
  • Gómara, M.J.; Canto, J.; Alsina, M.A.; Haro, I.; Perez, J.J. Conformational study of the pentadecapeptide 2F10 by circular dichroism, IR spectroscopy and molecular mechanics. Lett. Pept. Sci., 2000, 7, 255-262.
  • Saez-Torres, I.; Espejo, C.; Perez, J.J.; Acarin, N.; Montalban, X.; Martinez-Caceres, M. Peptide T does not ameliorate experimental autoimmune encephalomyelitis (EAE) in Lewis rats. Clin. Exper. Immunol., 2000, 121, 151-156.
  • Gomez-Catalan, J.; Alemán, C.; Perez, J.J. Conformational profile of 1-aminocyclopropanecarboxylic acid. Theor. Chem. Acc., 2000, 103, 380-389.
  • Perez, J.J.; Filizola, M.; Corcho, F. Docking of Peptide T onto the D1 domain of the Cd4 receptor. J. Biomol. Struct. Dyn., 2000, 17, 725-733.
  • Jimenez, A.I.; Cativiela, C.; Gomez-Catalan, J.; Perez, J.J.; Aubry, A.; Paris, M.; Marraud, M. Influence of side chain restriction and NH…π interaction on the β-turn folding modes of dipeptides incorporating phenylalanine cyclohexane derivatives. J, Am. Chem. Soc., 2000, 122, 5811-5821
  • Palomer, A.; Perez, J.J.; Navea, S,; Llorens, O.; Pascual, J.; Garcia, Ll.; Mauleon, D. Modeling cyclooxygenase inhibition. Implication of active site hydration on the selectivity of ketoprofen analogs. J. Med. Chem., 2000, 43, 2280-2284.
  • Bosch, J.; Roca, T.; Catena, J.-L.; Llorens, O.; Perez, J.J.; Lagunas, C.; Fernandez, A.G.; Miquel, I.; Fernandez-Serrat, A.; Farrerons, C. Synthesis and biological evaluation of 1,3,4-triaryl-3-pyrrolin-2-ones, a new class of selective cyclooxygenase-2 inhibitors. Bioorg. Med. Chem. Lett., 2000, 10, 1745-1748.
  • Corcho, F.; Filizola, M.; Perez, J.J. Evaluation of the iterative simulated annealing technique in conformational search of peptides. Chem. Phys. Lett., 2000, 319, 65-70.
  • Llorens, O.; Perez, J.J.; Palomer, A.; Mauleon, D. Structural basis of the dynamic mechanism of ligand binding to cyclooxygenase. Bioorg. Med. Chem. Lett., 1999, 9, 2779-27884
  • Corcho, F.; Filizola, M.; Perez, J.J. Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods. J. Biomol. Struct. Dyn., 1999, 16, 1043-1052.
  • Millet, O.; Perez, J.J. Pons, M. An easy NMR method to study the formation of parallel beta-sheets in peptide aggregates. Lett. Pept. Sci., 1999, 5, 1-7.
  • Cantó, J. ; Fernandez, Y.; Pons, M.; Giralt, E.; Perez, J.J. Molecular dynamics study of kaliotoxin in water. Int. J. Biol. Macromol., 1999, 24, núm. 1, 1-19.
  • Filizola, M.; Carteni-Farina, M.; Perez, J.J. Molecular modelling study of the differential ligand -receptor interaction at the mu, delta and kappa opiod receptors. J. Comput.-Aided Mol. Design, 1999, 13, 397-407.
  • Gomez-Catalan, J.; Perez, J.J.; Jimenez, A.I.; Cativiela, A. Study of the conformational profile of selected unnnatural aminoacid residues derived from L-phenylalanine. J. Pept. Sci., 1999, 5, 251-262.
  • Filizola, M.; Carteni-Farina, M.; Perez, J.J. Modelling the 3D structure of rhodopsin using a de novo approach to build G-protein coupled receptors. J. Phys. Chem. B, 1999, 103, 2520-2527.
  • Centeno, N.; Perez, J.J. A proposed bioactive form of peptide T. J. Comput.-Aided Mol. Design, 1998, 12, 7-14.
  • Filizola, M.; Rosell, G.; Guerrero, A.; Perez, J.J. Conformational requirements for inhibition of the pheromone catabolism in Spodoptera littoralis. Quant. Struct.-Activity Rel., 1998, 17, 205-210.
  • Perez, J.A.; Canto, J.; Reig, F.; Perez, J.J.; Haro, I. Conformational behavior of the HAV-VP3(110-121) peptidic sequence and synthetic analogs in membrane environments studied by CD and computational methods. Biopolymers, 1998, 45, 479-492.
  • Llorens, O, Centeno, N.B.; Filizola, M.; Spisani, S.; Marastoni, M; Calafell, M.; Herranz, C.; Perez, J.J. A proposed bioactive form of peptide T and the design of peptidomimetics. Lett. Pept. Sci., 1998, 5, 179-182.
  • Llorens, O. Filizola, M.; Spisani, S; Marastoni, M.; Herranz, C.; Perez, J.J. Amygdalin binds to the CD4 receptor as suggested from molecular modeling studies. Bioorg. Med. Chem. Lett., 1998, 8, 781-786.
  • Filizola, M.; Llorens, O.; Carteni-Farina, M.; Perez, J.J. New insights into the conformational requirements of B2 bradykinin antagonism. Bioorg. Med. Chem. Lett., 1998, 6, 1491-1500.
  • Filizola, M.; Perez, J.J.; Carteni-Farina, A. BUNDLE: A program for building the transmembrane domains of G-protein coupled receptors. J. Comput.-Aided Mol. Design, 1998, 12, 111-118.
  • Filizola, M.; Centeno, N.B.; Carteni-Farina, M.; Perez, J.J. Conformational analysis of the highly potent bradykinin antagonist HOE-140 by means of two different computational methods. J. Biomol. Struct. Dyn., 1998, 4, 639-652.
  • Cantó, J.; Perez, J.A.; Centeno, N.B.; Haro, I.; Perez, J.J. Conformational study of the preferred conformations of the peptide sequence VP3(110-121) of HAV by circular dichroism and molecular mechanics. Lett. Pept. Sci., 1997, 4, 13-19.
  • Filizola, M.; Perez, J.J.; Palomer, A.; Mauleon, D. Comparative molecular modelling study of the three-dimesional structures of prostaglandin endoperoxide H2 synthase 1 and 2 (COX-1 and COX-2). J. Mol. Graph., 1997, 15, 290-300.
  • Hinchliffe, A.; Perez, J.J.; Soscun-Machado, H.J. Density functional studies of molecular polarizabilities Part 4. The C10H8 molecules azulene, fluvalene and naphtalene. Elect. J. Theor. Chem., 1997, 2, 325-336.
  • Filizola, M.; Carteni-Farina, M.; Perez, J.J. Conformational Study of Vasoactive Intestinal peptide (VIP) by computational methods. J. Pept. Res., 1997, 50, 55-64.
  • Filizola, M.; Centeno, N.; Perez, J.J. Computational Study of the conformational domains of peptide T. J. Pept. Sci., 1997, 3, 85-92.
  • Perez, J.J.; Sadlej, A. Ab initio calculations of the polarizability of some aromatic molecules. J. Mol. Struct. (THEOCHEM), 1996, 371, 31-36.
  • Perez, J.J.; Centeno, N. New insights into the multiple minime problem. J. Mol. Struct. (THEOCHEM), 1996, 370, 173-179.
  • Perez, J.J.; Sharkey, M.; Centeno, N. On the bioactive conformation of small peptide and its set of thermodynamically accessible conformations. J. Biomol. Struct. Dyn., 1996, 14, 1-7.
  • Chao, T.; Perez, J.J.; Loew, G. Characterization of the Bioactive Form of Linear Peptide Antagonists at the &-opioid Receptor. Biopolymers, 1996, 38, 759-768.
  • Fernandez, Y.; Ricart, J.; Perez, J.J. Computational study of the conformational profiles of modelbis-cystine cyclic peptides. Int. J. Biol. Macromol., 1996, 18, 263-274.
  • Alemán, C.; Perez, J.J. A comparative study of the performance of Dewar’s semiempirical methods to compute electron spin resonance hyperfine coupling constants. THEOCHEM-J. Mol. Struct., 1996, 282, 251-258.
  • Alkorta, I.; Perez, J.J. Molecular Polarization Potential Maps of the Nucleic Acid Bases. Int. J. Quantum Chem., 1996, 57, 123-135.
  • Alkorta, I; Perez, J.J. Approximations in the computation of molecular polarization maps. Elect. J. Theor. Chem., 1995, 1, 26-37.
  • Perez, J.J.; Sanchez, Y.M. Centeno, N.B. Characterization of the conformational domains of bradykinin by computational methods. J. Pept. Sci., 1995, 1, 227-235.
  • Centeno, N.B.; Perez, J.J. New insights into the multiple minima problem associated with the conformational space of peptides. Chem. Phys. Lett., 1995, 232, 374-378.
  • Schove, L.; Perez, J.J.; Loew, G.H. Molecular determinants of recognition and activation of the cerebellar benzodiazepine receptor. Bioorg. Med. Chem. Lett., 1994, 2, 1029-1049.
  • Huang, P.; Perez, J.J.; Loew, G.H. Molecular dynamics simulations of phospholipids bilayers. J. Biomol. Struct. Dyn., 1994, 11, 927-956.
  • Alkorta, I.; Perez, J.J.; Villar, H. Molecular polarization maps as a tool for drug design and in chemical reactivity studies. J. Mol. Graph., 1994, 12, 3-13.
  • Alkorta, I.; Bachs, M.; Perez, J.J. The induced polarization of the water molecule. Chem. Phys. Lett., 1994, 224, 160-165.
  • Alemán, C.; Bella, J.; Perez, J.J. Molecular mechanics and molecular dynamics simulations of the hexagonal crystallyne form of the helical polyamide poly-(alpha-isobutyl-l-aspartate). Polymers, 1994, 35, 2596-2599.
  • Shove, L., Perez, J.J.; Maguire, P.A.; Loew, G.H. A new, novel class of benzodiazepine ligands based on CGS8216. Med. Chem. Res., 1994, 4, 307.
  • Mateu, M.; Hernandez, J.; Martinez, M.A.; Feigelstock, D.; Le, s.; Perez, J.J.; Giralt, E.; Stuart, D.; Palma, E.L.; Domingo, E. Antigenic heterogeneity of a foot-and-mouth disease virus serotype in the field is mediated by very limited sequence variation at several antigenic sites. J. Virol., 1994, 68, 1407-1417.
  • Alemán, C.; Perez, J.J. Conformational study of alanine and α-aminoisobutyric ψ[NHCO]-retroamide peptide analogues. Int. J. Pept. Prot. Res., 1994, 43, 258-263.
  • Perez, J.J.; Villar, H.; Arteca, G. Distribution of conformational energy minima in molecules with multiple torsional degrees of freedom. J. Phys. Chem., 1994, 98, 2318-2324.
  • Alemán, C.; Perez, J.J. SCF-MO study of the preferred conformations of nylons 1,N. J. Mol. Struct., 1994, 304, 17-24.
  • Alemán, C.; Perez, J.J. SCF-MO study of the polyhydration of N,N’-dimethylmalonamide. Int. J. Pept. Protein Res., 1993, 41, 606-610.
  • Alemán, C.; Perez, J.J. A Conformational study of the dehydroalanine dipeptide and homopolypeptide. Biopolymers, 1993, 33, 1811-1817
  • Aleman, C; Brillas, E; Davies, A. G.; Fajari, L.; Giro, D.; Julia, L.; Perez, J.J.; Rius, J. 2,2'-bithienyl derivatives - EPR investigation of their radical ions in solution, electrochemical properties, and crystal-structure J. Org. Chem., 1993, 58, 3091-3099
  • Alemán, C.; Perez, J.J. SCF-MO study of the polyglycine-II structure . J. Comp.-Aided Mol. Design, 1993, 7, 241-250
  • Maguire, P.A.; Perez, J.J.; Tsai, N.F.; Rodriguez, L.; Beatty, M.F.; Villar, H.O.; Kamal, J:J.; Upton, C.; Casy, A.F.; Loew, G.H. Molecular mechanism of delta-selectivity of indole analogs of non-peptide opioids. Mol. Pharmacol., 1993, 44, 1246-1251.
  • Vega, C.; Alemán, C.; Alhambra, C.; Perez, J.J. Effects of different continuum dielectric models in a molecular dynamics and energy minimization study of the antigenic loop of the FMDV. J. Biomol. Struct. Dyn., 1993, 11, 429-441.
  • Alkorta, I.; Villar, H.; Perez, J.J. Comparison of methods to estimate the free energy of solvation: importance in the modulation of the affinity of 3-benzazapines for the d1 receptor. J. Comput. Chem., 1993, 14, 620-626.
  • Aleman, C; Perez, J.J. Helical region of the potential energy surface of α-aminoisobutyric acid: a theoretical study. Int. J. Quantum Chem., 1993, 47, 231-238
  • Alemán, C.; Perez, J.J. SCF-MO study of the preferred conformation of a symmetric malonamide derivative N,N-dimethyl malonamide. J. Mol. Struct., 1993, 285, 221-227.
  • Alkorta, I.; Villar, H.; Perez, J.J. Effect of the basis set on the computation of molecular polarization. J. Phys. Chem., 1993, 97, 9113-9119.
  • Alemán, C.; Perez, J.J.; Vega, M.C. On the reliability of MINDO/3, MNDO and AM1 radical geometries for the computation of indo ESR hyperfine coupling constants. THEOCHEM-J. Mol. Struct., 1993, 281, 39-44.
  • Perez, J.J.; Villar, H.O.; Uyeno, E.; Toll, L.; Olsen, C.; Polgar, W.; Loew, G.H. Molecular determinants of recognition and activation at the μ-opioid receptor by Met-enkephalin-like peptides. Int. J. Quantum Chem., 1993, S20, 147-160.
  • Aleman, C; Perez, J.J.; Hinchliffe, A. Ab initio SCF-MO incremental triplet polarizabilities of neon clusters. international journal of mass spectrometry and ion processes, 1992, 122, 331-336.
  • Vega, C.; Alemán, C.; Perez, J.J. Conformational study of a nine residue fragment of the antigenic loop of foot. J. Biomol. Struct. Dyn., 1992, 10, 1-13.
  • Alemán, C.; Subirana, J.; Perez, J.J. A molecular mechanical study of the structure of poly(α-aminoisobutyric acid). Biopolymers, 1992, 32, 621-631.
  • Casas, I.; Perez, J.J. Modification to flow chart to determine point groups. J. Chem. Educ., 1992, 69,83.
  • Perez, J.J; Loew, G.H.; Villar, H.O. Influence of the ionization state on the conformation of Met-enkephalin. Int. J. Quantum Chem., 1992, 44, 263-275
  • Perez, J.J.; Villar, H.O.; Loew, G.H. Characterization of low-energy conformational domains for Met-enkephalin. J. Comput.-Aided Mol. Design, 1992, 6, 175-190.
  • Fernandez, Y; Perez, J.J; Ricart, J.M. A molecular mechanical study of the stability of Lys-Ala-Ala tripeptide. Int. J. Biol. Macromol., 1992, 14, 154-160.
  • Perez, J.J.; Villar, H.O. Computation of the polarizability of anthracene. Chem. Phys. Lett., 1992, 188, 604-608
  • Perez, J.J.; Alemán, C.; Hinchliffe, A. Ab initio MO calculations of incremental triple polarizabilities of alkali-metal halide clusters. J. Phys. Chem., 1991, 95, 9791-9794
  • Perez, J.J.; Ricart, J.M.; Masip, J. Conformational study of signal peptides of the lamb protein Int. J. Biol. Macromol. 1991, 13, 241-246
  • Loew, G.H.; Villar, H.O.; Cometta, C.; Perez, J.J. Conformational and electronic-properties of met-enkephalin. Int. J. Quantum Chem. 1991, 18, S165-S181
  • Perez, J.; Dupuis, M. Hydrogen-bonds and (hyper)polarizabilities in molecular-crystals - an ab initio SCF study of urea . J. Phys. Chem. 1991, 95, 6525-6529
  • Diez, J.; Davila, M.; Escarmis, C.; Mateu, M.G.; Dominguez, J.; Perez, J.J.; Giralt, E.; Melero, J.A.; Domingo, E. Unique amino-acid substitutions in the capsid proteins of foot-and-mouth-disease virus from a persistent infection in cell-culture. J. Virol. 1990, 64 , 5519-5528
  • Perez, J.J.; Portugal, J. Molecular modeling study of changes induced by netropsin binding to nucleosome core particles. Nucl. Acids Res. 1990, 18, 3731-3737
  • Ferrer, N; Perez, J.J. Determination of sources of atmospheric aerosol in the neighborhood of barcelona based on receptor models. Atmos. Environ. Part b-Urban atmosphere, 1990, 24, 181-184
  • Mota, F; Novoa, J.J.; Perez, J.J. Potential-energy surfaces for the Na+...CO2, K+...CO2 systems J. Mol. Struc. (Theochem). 1987, 34 193-200 Perez, J.J. Molecular aspects of atmospheric aerosols. Afinidad, 1986, 43, 477-479
  • Rubio, J.; Perez, J.J. Energy-levels in the jj coupling scheme. J. Chem. Educ. 1986, 63, 476-478
  • Ferrer, N; Perez, J.J. Sensitive method for bromide determination in atmospheric aerosols. J- Chromatog. 1986, 356, 464-467
  • Ferrer, N; Perez, J.J. Determining inorganic anions in the atmosphere by ion-exchange chromatography international. J. Environ. Anal. Chem. 1986, 27, 273-287
  • Mota, F.; Perez, J.J. The general contraction scheme on the evaluation of molecular polarizabilities J. Mol. Struc. (Theochem). 1985, 21, 365-370
  • Perez, J.J.; Clarke, J.H.R.; Hinchliffe, A. 3-body contributions to the dipole polarizability of He-3 clusters. Chem. Phys. Lett. 1984, 104, 583-586
  • Ricart, J.M.; Perez, J.J.; Pons, M.; Giralt, E. Conformational basis of N-glycosylation of proteins - conformational-analysis of Ac-Asn-Ala-Thr-NH2 Int. J. Biol. Macromol. 1983, 5, 279-282