List of works - Jaime Rubio-Martínez

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

scientific article published on 17 January 2018

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

scientific article published on 6 September 2016

Atomic level rendering of DNA-drug encounter.

scientific article

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

scientific article published on 12 May 2017

Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP-peptide complexes.

scientific article published in January 2007

Conformationally restricted hydantoin-based peptidomimetics as inhibitors of caspase-3 with basic groups allowed at the S3 enzyme subsite.

scientific article

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

scientific article

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

scientific article published on 28 February 2014

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

scientific article published on 12 March 2019

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

scientific article published on 12 October 2017

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

scientific article published on 15 November 2009

Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase.

scientific article

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

scientific article

Modeling and subtleties of K-Ras and Calmodulin interaction

scientific article published on 30 October 2018

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

scientific article published on 30 January 2020

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.

scientific article published on 15 April 2014

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.

scientific article

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.

scientific article

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

scientific article published on 23 October 2019

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

scientific article published on 29 December 2020

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

scientific article

Rational design of new class of BH3-mimetics as inhibitors of the Bcl-xL protein.

scientific article published on 13 May 2011

Reducing CDK4/6-p16(INK4a) interface. Computational alanine scanning of a peptide bound to CDK6 protein.

scientific article published in June 2006

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

scientific article published on 17 November 2012

Structural analysis of the inhibition of Cdk4 and Cdk6 by p16(INK4a) through molecular dynamics simulations

scientific article published on 01 December 2002

Structure-based approach to the design of BakBH3 mimetic peptides with increased helical propensity.

scientific article

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

scientific article

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

scientific article published on January 2011

Toward understanding calmodulin plasticity by molecular dynamics

scientific article published on 29 May 2019

List of works by Jaime Rubio-Martínez

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

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

Atomic level rendering of DNA-drug encounter.

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

Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP-peptide complexes.

Conformationally restricted hydantoin-based peptidomimetics as inhibitors of caspase-3 with basic groups allowed at the S3 enzyme subsite.

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

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

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

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

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

Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase.

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

Modeling and subtleties of K-Ras and Calmodulin interaction

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

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.

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.

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.

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

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

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

Rational design of new class of BH3-mimetics as inhibitors of the Bcl-xL protein.

Reducing CDK4/6-p16(INK4a) interface. Computational alanine scanning of a peptide bound to CDK6 protein.

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

Structural analysis of the inhibition of Cdk4 and Cdk6 by p16(INK4a) through molecular dynamics simulations

Structure-based approach to the design of BakBH3 mimetic peptides with increased helical propensity.

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

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

Toward understanding calmodulin plasticity by molecular dynamics