J. J. Pérez

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New Insights into the Stereochemical Requirements of the Bombesin BB1 Receptor Antagonists Binding

P. Gómez-Gutiérrez, B. Rasaeifar, J. J. Pérez, 2020, Pharmaceuticals.

Hydrogen bonds and (hyper)polarizabilities in molecular crystals : an ab initio SCF study of urea

M. Dupuis, J. J. Pérez, 1991 .

Calcium-induced decrease of the thermal stability and chaperone activity of α-crystallin

P. Garriga, L. J. Valle, C. Escribano, 2002 .

Molecular Mechanisms of Disease for Mutations at Gly-90 in Rhodopsin*

P. Garriga, M. Aguilà, M. Cheetham, 2011, The Journal of Biological Chemistry.

Potential energy surfaces for the X+⋯CO2 (X = Na, K) systems

F. Mota, J. Novoa, J. J. Pérez, 1987 .

The induced polarization of the water molecule

I. Alkorta, M. Bachs, J. J. Pérez, 1994 .

Effect of disulfide bonds in the conformation of cyclic dimer peptides

E. Giralt, C. García-echeverría, F. Albericio, 1991 .

Assessment of the Bioactive Conformation of the Vasoactive Intestinal Peptide by Computational Methods

M. Filizola, J. J. Pérez, 2002 .

Ab initio calculations of the polarizability of some aromatic molecules

A. J. Sadlej, J. J. Pérez, 1996 .

New insights into the multiple minima problem associated with the conformational space of peptides

N. B. Centeno, J. J. Pérez, 1995 .

Managing molecular diversity.

Juan J Perez, J. J. Pérez, 2005, Chemical Society reviews.

Synthesis and evaluation of diverse analogs of amygdalin as potential peptidomimetics of peptide T.

Alex Rodriguez, A. Spada, J. Pérez, 2005, Bioorganic & medicinal chemistry letters.

A conformational study of the dehydroalanine: Dipeptide and homopolypeptide

C. Alemán, J. J. Pérez, 1993, Biopolymers.

Molecular dynamics simulations of Ac-3Aib-Cage-3Aib-NHMe

Parvesh Singh, P. Sharma, J. J. Pérez, 2010 .

Molecular determinants of the bacterial resistance to fluoroquinolones: a computational study.

P. Gómez-Gutiérrez, C. Lupala, J. J. Pérez, 2013, Current computer-aided drug design.

N-acetyl-N'-methylamide derivative of (2S,3S)-1-amino-2,3-diphenylcyclopropanecarboxylic acid: theoretical analysis of the conformational impact produced by the incorporation of the second phenyl group to the cyclopropane analogue of phenylalanine.

Jordi Casanovas, Carlos Alemán, Carlos Cativiela, 2003, The Journal of organic chemistry.

Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituents.

Carlos Aleman, Jordi Casanovas, Carlos Cativiela, 2006, The journal of physical chemistry. B.

Influence of the Phenyl Side Chain on the Conformation of Cyclopropane Analogues of Phenylalanine

Jordi Casanovas, Carlos Alemán, Juan J. Perez, 2002 .

Influence of Side Chain Restriction and NH···π Interaction on the β-Turn Folding Modes of Dipeptides Incorporating Phenylalanine Cyclohexane Derivatives

A. Aubry, C. Cativiela, A. Jiménez, 2000 .

Simulated annealing study of the pentacyclo-undecane cage amino acid tripeptides of the type [Ac-X-Y-Z-NHMe]

J. Cantó, F. Corcho, H. G. Kruger, 2006 .

Design of Peptidomimetics

Jaime Rubio-Martinez, Juan J. Perez, Francesc J. Corcho, 2010 .

Molecular polarization potential maps of the nucleic acid bases

Ibon Alkorta, Juan J. Perez, I. Alkorta, 1996 .

On the reliability of MINDO/3, MNDO and AM1 radical geometries for the computation of INDO electron spin resonance hyperfine coupling constants

C. Alemán, M. C. Vega, J. J. Pérez, 1993 .

Conformational ensembles of neuromedin C reveal a progressive coil-helix transition within a binding-induced folding mechanism.

K. Pauwels, P. Sanchís, B. Vilanova, 2015 .

Conformational analysis of small peptides of the type Ac–X–NHMe, where X=Gly, Ala, Aib and Cage

J. J. Pérez, J. Catalán, Krishna. Bisetty, 2005 .

Characterization of the bioactive form of linear peptide antagonists at the δ‐opioid receptor

Juan J. Perez, Gilda H. Loew, G. Loew, 1996 .

Blockade of the Interaction of Calcineurin with FOXO in Astrocytes Protects Against Amyloid-β-Induced Neuronal Death.

R. Hervás, J. Vitorica, I. Torres Alemán, 2016, Journal of Alzheimer's disease : JAD.

Conformational basis of N-glycosylation of proteins: conformational analysis of Ac-Asn-Ala-Thr-NH2

E. Giralt, M. Pons, J. Pérez, 1983 .

A methyl group at C7 of 11-cis-retinal allows chromophore formation but affects rhodopsin activation

P. Garriga, A. Lera, R. Álvarez, 2006, Vision Research.

Conformational diversity in contryphans from Conus venom: cis-trans isomerisation and aromatic/proline interactions in the 23-membered ring of a 7-residue peptide disulfide loop.

Alex Rodriguez, P. Balaram, K. H. Gowd, 2013, Chemistry.

A comparative study of the performance of Dewar's semiempirical methods to compute electron spin resonance hyperfine coupling constants

C. Alemán, M. C. Vega, J. J. Pérez, 1993 .

A proposed bioactive form of peptide T and the design of peptidomimetics

M. Filizola, M. Calafell, N. B. Centeno, 1998, Letters in Peptide Science.

Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations.

M. S. Tomás, J. Rubio-Martínez, J. J. Pérez, 2017, Journal of molecular graphics & modelling.

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

Juan Jesús Pérez, Jaime Rubio-Martinez, Marta Pinto, 2004, J. Comput. Aided Mol. Des..

Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering

Alberto Pérez, R. Pérez, J. J. Pérez, 2021, Frontiers in Molecular Biosciences.

Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase

J. Pérez, J. Rubio-Martínez, P. Gómez-Gutiérrez, 2017, J. Chem. Inf. Model..

Discovery of Diverse Natural Products as Inhibitors of SARS-CoV-2 Mpro Protease through Virtual Screening

O. Abián, A. Velázquez‐Campoy, S. Vega, 2021, J. Chem. Inf. Model..

New insights into the stereochemical requirements of the bradykinin B1 receptor antagonists binding.

J. Pérez, P. Gómez-Gutiérrez, C. Lupala, 2016, Journal of molecular graphics & modelling.

New insights into the stereochemical requirements of the bradykinin B2 receptor antagonists binding

Juan Jesús Pérez, Cecylia S. Lupala, Patricia Gomez-Gutierrez, 2016, Journal of Computer-Aided Molecular Design.

Designing type II topoisomerase inhibitors: A molecular modeling approach.

P. Gómez-Gutiérrez, C. Lupala, J. J. Pérez, 2013, Current topics in medicinal chemistry.

Exploiting Knowledge on Structure–Activity Relationships for Designing Peptidomimetics of Endogenous Peptides

J. J. Pérez, 2021, Biomedicines.

of Computer-Aided Molecular Design NEW INSIGHTS INTO THE STEREOCHEMICAL REQUIREMENTS OF THE BRADYKININ B 2 RECEPTOR ANTAGONISTS

P. Gómez-Gutiérrez, C. Lupala, J. J. Pérez, 2015 .

Iodine Atoms: A New Molecular Feature for the Design of Potent Transthyretin Fibrillogenesis Inhibitors

M. Saraiva, J. Pérez, J. T. Vázquez, 2009, PloS one.

Molecular Modeling of the M3 Acetylcholine Muscarinic Receptor and Its Binding Site

Juan J. Perez, Marlet Martinez-Archundia, Pere Garriga, 2012, Journal of biomedicine & biotechnology.

An Assessment of the Conformational Profile of Neuromedin B Using Different Computational Sampling Procedures

Krishna Bisetty, J. Pérez, Parvesh Singh, 2012 .

Energy levels in the jj coupling scheme

J. Rubio, J. J. Pérez, 1986 .

Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers.

O. Edholm, A. Cordomí, J. J. Pérez, 2009, Journal of chemical theory and computation.

Effect of ions on a dipalmitoyl phosphatidylcholine bilayer. a molecular dynamics simulation study.

Arnau Cordomí, Juan J Perez, Olle Edholm, 2008, The journal of physical chemistry. B.

Structural Study of a New HIV-1 Entry Inhibitor and Interaction with the HIV-1 Fusion Peptide in Dodecylphosphocholine Micelles.

I. Haro, E. Yuste, Yolanda Pérez, 2017, Chemistry.

Is the Folding Topology of a Protein Related to its Amino Acid Occurrence?

J. J. Pérez, 2011, Journal of biomolecular structure & dynamics.

An easy NMR method to study the formation of parallel β-sheets in peptide aggregates

M. Pons, J. J. Pérez, Ó. Millet, 1999, Letters in Peptide Science.

Molecular Polarization Potential as a Molecular Descriptor to Predict Biological Activity of Dioxins and Dibenzofurans

L. Roset, J. J. Pérez, 2016, Molecular informatics.

Zinc Is Involved in Depression by Modulating G Protein-Coupled Receptor Heterodimerization

P. Garriga, K. Koch, C. Lupala, 2016, Molecular Neurobiology.

Effect of different treatments of long‐range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer

Juan Jesús Pérez, Arnau Cordomí, Olle Edholm, 2007, J. Comput. Chem..

SCF-MO study of the preferred conformations of nylons 1,n

C. Alemán, J. J. Pérez, 1994 .

SCF-MO study of the preferred conformation of a symmetric malonamide derivative: N,N' -dimethyl malonamide

C. Alemán, J. J. Pérez, 1993 .

SCF-MO study of the polyglycine II structure

Juan Jesús Pérez, Carlos Alemán, C. Alemán, 1993, J. Comput. Aided Mol. Des..

Identification of a Novel Inhibitory Allosteric Site in p38α

P. Gómez-Gutiérrez, M. Vega, J. J. Pérez, 2016, PloS one.

Structural Rearrangements of Rhodopsin Subunits in a Dimer Complex: a Molecular Dynamics Simulation Study

A. Cordomí, J. J. Pérez, 2009, Journal of biomolecular structure & dynamics.

Molecular Dynamics Simulations of Rhodopsin Point Mutants at the Cytoplasmic Side of Helices 3 and 6

P. Garriga, A. Cordomí, E. Ramon, 2008, Journal of biomolecular structure & dynamics.

Critical Role of Electrostatic Interactions of Amino Acids at the Cytoplasmic Region of Helices 3 and 6 in Rhodopsin Conformational Properties and Activation*

P. Garriga, A. Cordomí, I. I. Senin, 2007, Journal of Biological Chemistry.

Amygdalin analogs for the treatment of psoriasis.

J. J. Pérez, 2013, Future medicinal chemistry.

Structural Analysis of the Inhibition of Cdk4 and Cdk6 by p16INK4a through Molecular Dynamics Simulations

Óscar Villacañas, J. Pérez, J. Rubio-Martínez, 2002, Journal of biomolecular structure & dynamics.

Identification of selective inhibitors of acetylcholinesterase from a combinatorial library of 2,5-piperazinediones

F. Sánchez-Baeza, E. Pérez-Payá, F. Corcho, 2000, Molecular Diversity.

Flavonoid allosteric modulation of mutated visual rhodopsin associated with retinitis pigmentosa

P. Garriga, J. Pérez, C. Lupala, 2017, Scientific Reports.

Discovery of a Bradykinin B2 Partial Agonist Profile of Raloxifene in a Drug Repurposing Campaign

P. Gómez-Gutiérrez, J. J. Pérez, 2020, International journal of molecular sciences.

Importance of structure-based studies for the design of a novel HIV-1 inhibitor peptide

P. Ziprin, A. Meyerhans, C. Herrera, 2020, Scientific Reports.

Assessment of the conformational profile of bombesin by computational methods.

P. Gómez-Gutiérrez, A. Valverde, J. J. Pérez, 2020, Journal of molecular graphics & modelling.

Topical application of an amygdalin analogue reduces inflammation and keratinocyte proliferation in a psoriasis mouse model

E. Wagner, Nuria Gago-López, J. J. Pérez, 2021, Experimental dermatology.

Molecular modeling study of the differential ligand–receptor interaction at the μ, δ and κ opioid receptors

Marta Filizola, Juan J. Perez, Maria Carteni-Farina, 1999, J. Comput. Aided Mol. Des..

Designing Peptidomimetics.

J. J. Pérez, 2018, Current topics in medicinal chemistry.

The general contraction scheme on the evaluation of molecular polarizabilities

F. Mota, J. Pérez, J. J. Pérez, 1985 .

Characterization of low-energy conformational domains for Met-enkephalin

Hugo O. Villar, Gilda H. Loew, Juan J. Perez, 1992, J. Comput. Aided Mol. Des..

Conformational and electronic properties of met-enkephalin

H. Villar, G. Loew, J. J. Pérez, 1991 .

Fragment dissolved molecular dynamics: a systematic and efficient method to locate binding sites.

J. Rubio-Martínez, J. Bonet, J. M. Granadino-Roldán, 2021, Physical chemistry chemical physics : PCCP.

Effect of Sodium Valproate on the Conformational Stability of the Visual G Protein-Coupled Receptor Rhodopsin

P. Garriga, Pol Fernandez-Gonzalez, Aina Mas-Sanchez, 2021, Molecules.

EFFECT OF THE LIGAND IN THE MODELING THE 3 D STRUCTURE OF THE M 3 MUSCARINIC RECEPTOR BAHAREH RASAEIFAR

B. Rasaeifar, J. J. Pérez, 2013 .

Helical region of the potential energy surface of α-aminoisobutyric acid: A theoretical study

C. Alemán, J. J. Pérez, 1993 .

Peptidic Scaffolds Enable Rapid and Multivariate Secondary Sphere Evolution for an Abiotic Metallocatalyst.

Andy I. Nguyen, D. McElheny, J. Pérez, 2022, Inorganic chemistry.

Comparative structural studies of T-20 analogues using molecular dynamics

F. Corcho, Parvesh Singh, P. Sharma, 2011 .

Conformational profile of bombesin assessed using different computational protocols.

F. Corcho, Parvesh Singh, P. Sharma, 2010, Journal of molecular graphics & modelling.

Ab initio SCF-MO incremental triplet polarizabilities of neon clusters

C. Alemán, J. Pérez, A. Hinchliffe, 1992 .

Conformational study of alanine and α‐aminoisobutyric Ψ[NHCO]‐retroamide peptide analogues

C. Alemán, J. J. Pérez, 2009 .

Assessment of the Sampling Performance of Multiple-Copy Dynamics versus a Unique Trajectory

Juan Jesús Pérez, M. Santos Tomás, Jaime Rubio-Martinez, 2016, J. Chem. Inf. Model..

Effect of automation on the accuracy of alchemical free energy calculation protocols

Jaime Rubio-Martinez, Julien Michel, Stefano Bosisio, 2018 .

A computational study of Neuromedin B

Parvesh Singh, P. Sharma, J. J. Pérez, 2011 .

A molecular mechanical study of the structure of poly(α‐aminoisobutyric acid)

C. Alemán, J. A. Subirana, J. J. Pérez, 1992 .

Computation of the polarizability of anthracene

H. Villar, J. Pérez, J. J. Pérez, 1992 .

Three-body contributions to the dipole polarizability of He3 clusters

A. Hinchliffe, J. Clarke, J. J. Pérez, 1984 .

A molecular dynamics study of the pentacyclo-undecane cage amino acid tripeptide

J. Cantó, F. Corcho, J. J. Pérez, 2006 .

Computational study of the conformational preferences of the (R)‐8‐amino‐pentacyclo[5.4.0.02,6.03,10.05,9] undecane‐8‐carboxylic acid monopeptide

C. Alemán, E. Giralt, J. Gómez-catalán, 2004, Journal of peptide science : an official publication of the European Peptide Society.

Amygdalin Analogues Inhibit IFN-γ Signalling and Reduce the Inflammatory Response in Human Epidermal Keratinocytes

G. Donnarumma, I. Paoletti, M. Tufano, 2013, Inflammation.

Comparison of methods to estimate the free energy of solvation:Importance in the modulation of the affinity of 3‐benzazepines for the D1receptor

Juan Jesús Pérez, Hugo O. Villar, Ibon Alkorta, 1993, J. Comput. Chem..

Assessment of the bound conformation of Bombesin to the BB1 and BB2 Receptors

J. Rubio-Martínez, J. J. Pérez, Guillem Vila-Julià, 2023, bioRxiv.

Mercury-induced dark-state instability and photobleaching alterations of the visual g-protein coupled receptor rhodopsin.

P. Garriga, Darwin Toledo, Margarita Morillo, 2014, Chemical research in toxicology.

BUNDLE: A program for building the transmembrane domains of G-protein-coupled receptors

Juan Jesús Pérez, Marta Filizola, Maria Cartenì-Farina, 1998, J. Comput. Aided Mol. Des..

Calcium-induced decrease of the thermal stability and chaperone activity of alpha-crystallin.

P. Garriga, L. D. Del Valle, C. Escribano, 2002, Biochimica et biophysica acta.

Rational Design of New Class of BH3-Mimetics As Inhibitors of the Bcl-xL Protein

Juan Jesús Pérez, Jaime Rubio-Martinez, Marta Pinto, 2011, J. Chem. Inf. Model..

Molecular dynamics simulations of phospholipid bilayers.

P. Huang, G. Loew, J. J. Pérez, 1994, Journal of biomolecular structure & dynamics.

A Step Forward toward Selective Activation/Inhibition of Bak, a Pro-Apoptotic Member of the Bcl-2 Protein Family: Discovery of New Prospective Allosteric Sites Using Molecular Dynamics

J. Rubio-Martínez, J. J. Pérez, Guillem Vila-Julià, 2023, J. Chem. Inf. Model..

Randomized tree construction algorithm to explore energy landscapes

Juan Cortés, Juan Jesús Pérez, Léonard Jaillet, 2011, J. Comput. Chem..

Investigation of structural and electronic biases in mutagenic compounds

Hugo O. Villar, Juan J. Perez, H. Villar, 2002 .

Rational Design of New Class of BH3-Mimetics As Inhibitors of the Bcl-xL Protein

J. Rubio-Martínez, M. Pinto, M. Orzáez, 2011, J. Chem. Inf. Model..

Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling

J. Pérez, P. Gómez-Gutiérrez, C. Lupala, 2018, Journal of biomolecular structure & dynamics.

New insights into the molecular mechanism of rhodopsin retinitis pigmentosa from the biochemical and functional characterization of G90V, Y102H and I307N mutations

P. Garriga, L. Bosch-Presegué, Pol Fernandez-Gonzalez, 2022, Cellular and Molecular Life Sciences.

Differential binding mode of diverse cyclooxygenase inhibitors.

Juan J Perez, Albert Palomer, D. Mauleón, 2002, Journal of molecular graphics & modelling.

Complete maps of molecular‐loop conformational spaces

Juan Jesús Pérez, Federico Thomas, Francesc Corcho, 2008, J. Comput. Chem..

Complete maps of molecular‐loop conformational spaces

Juan Jesús Pérez, Federico Thomas, Francesc Corcho, 2007, J. Comput. Chem..

Interactions of fatty acids with phosphatidylethanolamine membranes: X-ray diffraction and molecular dynamics studies

P. Escribá, S. Funari, J. Frau, 2010, Journal of Lipid Research.

Molecular Determinants for the Activation/Inhibition of Bak Protein by BH3 Peptides

Juan Jesús Pérez, Jaime Rubio-Martinez, José M. Granadino-Roldán, 2020, J. Chem. Inf. Model..

Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers.

A. Cordomí, J. J. Pérez, 2007, Journal of Physical Chemistry B.

Zinc Is Involved in Depression by Modulating G Protein-Coupled Receptor Heterodimerization

P. Garriga, K. Koch, C. Lupala, 2015, Molecular Neurobiology.

Evaluation of the iterative simulated annealing technique in conformational search of peptides

Marta Filizola, Juan J. Perez, Francesc J. Corcho, 2000 .

A general procedure for building the transmembrane domains of G‐protein coupled receptors

M. Filizola, J. J. Pérez, Maria Caritenì‐Farina, 1998 .

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.

C. Alemán, C. Cativiela, A. Jiménez, 2005, The journal of physical chemistry. B.

Molecular modeling in the design of peptidomimetics and peptide surrogates.

Francesc Corcho, Juan J Perez, F. Corcho, 2002, Current medicinal chemistry.

Antigenic Heterogeneity ofaFoot-and-Mouth Disease Virus Serotype intheField IsMediated byVeryLimited Sequence Variation atSeveral Antigenic Sites

D. Stuart, E. Giralt, M. G. Mateu, 1994 .

Molecular Features of Non-Selective Small Molecule Antagonists of the Bradykinin Receptors

P. Gómez-Gutiérrez, B. Rasaeifar, J. J. Pérez, 2020, Pharmaceuticals.