J. Rubio-Martínez

发表

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.

A benchmark calculation for the fuzzy c-means clustering algorithm: initial memberships

Jaime Rubio-Martinez, Alex Rodriguez, M. S. Tomás, 2012, Journal of Mathematical Chemistry.

Reducing CDK4/6‐p16INK4a interface. Computational alanine scanning of a peptide bound to CDK6 protein

Óscar Villacañas, J. Rubio-Martínez, 2006, Proteins.

Atomic level rendering of DNA-drug encounter.

V. Guallar, M. Lucas, J. Rubio-Martínez, 2014, Biophysical journal.

Design of novel ligands of CDP‐methylerythritol kinase by mimicking direct protein‐protein and solvent‐mediated interactions

Óscar Villacañas, J. Rubio-Martínez, Meritxell Antolín-Llovera, 2011, Journal of molecular recognition : JMR.

Design of an interface peptide as new inhibitor of human glucose-6-phosphate dehydrogenase.

M. Cascante, Santiago Díaz-Moralli, J. Rubio-Martínez, 2014, Journal of molecular graphics & modelling.

Protein–protein recognition as a first step towards the inhibition of XIAP and Survivin anti‐apoptotic proteins

J. Rubio-Martínez, J. M. Granadino-Roldán, C. Obiol-Pardo, 2008, Journal of molecular recognition : JMR.

Mimicking direct protein–protein and solvent-mediated interactions in the CDP-methylerythritol kinase homodimer: a pharmacophore-directed virtual screening approach

Jaime Rubio-Martinez, Victor Giménez-Oya, Óscar Villacañas, 2009, Journal of molecular modeling.

Exploring potential energy surfaces with gentlest ascent dynamics in combination with the shrinking dimer method and Newtonian dynamics

J. M. Bofill, W. Quapp, J. Rubio-Martínez, 2018, Theoretical Chemistry Accounts.

Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase

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

Molecular dynamics analysis of the interaction between the human BCL6 BTB domain and its SMRT, NcoR and BCOR corepressors: the quest for a consensus dynamic pharmacophore.

J. Rubio-Martínez, J. M. Granadino-Roldán, A. Garzón, 2014, Journal of molecular graphics & modelling.

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

M. S. Tomás, J. Rubio-Martínez, J. M. Granadino-Roldán, 2015, Current computer-aided drug design.

Homology modeling of Mycobacterium tuberculosis 2C-methyl-d-erythritol-4-phosphate cytidylyltransferase, the third enzyme in the MEP pathway for isoprenoid biosynthesis

J. Rubio-Martínez, A. Cordero, C. Obiol-Pardo, 2010, Journal of molecular modeling.

Shedding light on the binding mechanism of kinase inhibitors BI-2536, Volasetib and Ro-3280 with their pharmacological target PLK1.

J. Rubio-Martínez, I. Bravo, J. Albaladejo, 2022, Journal of photochemistry and photobiology. B, Biology.

958PDOES THE PRESENCE OF HEPATITIS VIRUS B & C INFLUENCE THE EVOLUTION OF DIFFUSE LARGE B-CELL LYMPHOMAS?

J. Rubio-Martínez, V. Calvo, M. Palka, 2014, Annals of oncology : official journal of the European Society for Medical Oncology.

Assessment of the performance of cluster analysis grouping using pharmacophores as molecular descriptors

M. S. Tomás, Alex Rodriguez, J. Pérez, 2005 .

A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors.

J. Rubio-Martínez, J. M. Granadino-Roldán, A. Garzón, 2018, Future medicinal chemistry.

Molecular dynamics simulations of an α-synuclein NAC domain fragment with a ff14IDPSFF IDP-specific force field suggest β-sheet intermediate states of fibrillation.

J. Rubio-Martínez, F. Mas, S. Madurga, 2022, Physical chemistry chemical physics : PCCP.

Homology modeling of 2C-methyl–erythritol-4-phosphate cytidylyltransferase, the third enzyme in the MEP pathway for isoprenoid biosynthesis

J. Rubio-Martínez, C. Obiol-Pardo, S. Imperial, 2020 .

α4-α5 Helices on Surface of KRAS Can Accommodate Small Compounds That Increase KRAS Signaling While Inducing CRC Cell Death

N. Agell, J. Rubio-Martínez, Caroline Mauvezin, 2023, International journal of molecular sciences.

Predicting binding energies of CDK6 inhibitors in the hit-to-lead process

J. Rubio-Martínez, J. M. Granadino-Roldán, Javier Aríñez-Soriano, 2011 .

The methylerythritol phosphate (MEP) pathway for isoprenoid biosynthesis as a target for the development of new drugs against tuberculosis.

J. Rubio-Martínez, C. Obiol-Pardo, S. Imperial, 2011, Current medicinal chemistry.

Microwave‐Assisted Synthesis of Substituted Pyrrolo[2,3‐d]pyrimidines

J. Rubio-Martínez, G. Guillaumet, M. Font‐Bardia, 2014 .

Substituted tetrahydroisoquinolines: synthesis, characterization, antitumor activity and other biological properties.

D. Caignard, J. Rubio-Martínez, M. D. Pujol, 2018, European journal of medicinal chemistry.

One-pot synthesis of 4-aminated pyrrolo[2,3-d]pyrimidines from alkynylpyrimidines under metal-catalyst-free conditions

J. Rubio-Martínez, G. Guillaumet, M. D. Pujol, 2015 .

Homology modeling of human transketolase: description of critical sites useful for drug design and study of the cofactor binding mode.

J. Rubio-Martínez, C. Obiol-Pardo, 2009, Journal of molecular graphics & modelling.

Design of Peptidomimetics

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

Cyclin-dependent kinases 4 and 6 control tumor progression and direct glucose oxidation in the pentose cycle

M. Cascante, O. Bachs, N. Agell, 2012, Metabolomics.

Modeling and subtleties of K-Ras and Calmodulin interaction

Jaime Rubio-Martinez, Eduardo Garrido, Juan Lázaro, 2018, PLoS Comput. Biol..

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..

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..

A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance

J. Fernández-Recio, U. Eckhard, J. Rubio-Martínez, 2023, Science advances.

Binding of the anticancer drug BI-2536 to human serum albumin. A spectroscopic and theoretical study.

J. Rubio-Martínez, I. Bravo, J. Albaladejo, 2017, Journal of photochemistry and photobiology. B, Biology.

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

Jaime Rubio-Martinez, Marta Pinto, Laura Delgado-Soler, 2012, J. Chem. Inf. Model..

Molecular Topology Applied to the Discovery of 1-Benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a Non-Ligand-Binding-Pocket Antiandrogen

Jaime Rubio-Martinez, David G. Lloyd, Fernando Blanco, 2014, J. Chem. Inf. Model..

Comparative Evaluation of MMPBSA and XSCORE To Compute Binding Free Energy in XIAP-Peptide Complexes

Jaime Rubio-Martinez, Cristian Obiol-Pardo, J. Rubio-Martínez, 2007, J. Chem. Inf. Model..

Multigram scale synthesis of polycyclic lactones and evaluation of antitumor and other biological properties.

J. Rubio-Martínez, M. Viñas, J. Morral, 2020, European journal of medicinal chemistry.

Diphenyl Urea Derivatives as Inhibitors of Transketolase: A Structure-Based Virtual Screening

Jaime Rubio-Martinez, Marta Cascante, Cristian Obiol-Pardo, 2012, PloS one.

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.

Conformationally Restricted Hydantoin‐Based Peptidomimetics as Inhibitors of Caspase‐3 with Basic Groups Allowed at the S3 Enzyme Subsite

E. Pérez-Payá, F. Albericio, J. Rubio-Martínez, 2008, ChemMedChem.

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

J. Rubio-Martínez, Maite González-Mendióroz, A. Álvarez-Vázquez, 2013, Journal of molecular graphics & modelling.

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..

Pseudometrics from three-positive semidefinite similarities

M. Santos Tomás, Jaime Rubio-Martinez, Claudi Alsina, 2006, Fuzzy Sets Syst..

Autochthonous Peruvian Natural Plants as Potential SARS-CoV-2 Mpro Main Protease Inhibitors

O. Abián, A. Velázquez‐Campoy, S. Vega, 2023, Pharmaceuticals.

Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors

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

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

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

RED: A Set of Molecular Descriptors Based on Re'nyi Entropy

Raúl Toral, M. Santos Tomás, Jaime Rubio-Martinez, 2009, J. Chem. Inf. Model..

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

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

MA10.01 Antibiotic Use and PD-1 Inhibitors: Shorter Survival in Lung Cancer, Especially When Given Intravenously. Type of Infection Also Matters

J. Rubio-Martínez, R. L. Castro, E. Pérez-Fernández, 2018, Journal of Thoracic Oncology.

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..

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..

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..

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..

The Discovery of inhibitors of the SARS-CoV-2 S protein through computational drug repurposing.

J. Rubio-Martínez, J. M. Granadino-Roldán, João Zulaica, 2024, Computers in biology and medicine.

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

J. Rubio-Martínez, Juan J. Perez, M. Santos Tomas, 2017, Journal of molecular graphics & modelling.

On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

J. Rubio-Martínez, F. Mas, S. Madurga, 2020, Polymers.