List of works - Victor Guallar

A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding

scientific article

A new view of the bacterial cytosol environment

scientific article

A theoretical multiscale treatment of protein-protein electron transfer: The ferredoxin/ferredoxin-NADP(+) reductase and flavodoxin/ferredoxin-NADP(+) reductase systems

scientific article published on 16 September 2015

An alternative mechanism for the methylation of phosphoethanolamine catalyzed by Plasmodium falciparum phosphoethanolamine methyltransferase.

scientific article

An atomistic view on human hemoglobin carbon monoxide migration processes.

scientific article published on 21 February 2012

Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase.

scientific article published on 2 February 2015

AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design

scientific article published in 2023

Atomic level rendering of DNA-drug encounter.

scientific article

Atomic picture of ligand migration in toluene 4-monooxygenase

scientific article published on 13 May 2014

Atomistic simulations shed new light on the activation mechanisms of RORγ and classify it as Type III nuclear hormone receptor regarding ligand-binding paths

scientific article published on 21 November 2019

Basidiomycete DyPs: Genomic diversity, structural-functional aspects, reaction mechanism and environmental significance

scientific article

Binding of Thioflavin T and Related Probes to Polymorphic Models of Amyloid-β Fibrils.

scientific article published on 29 August 2017

Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.

scientific article published on March 2015

Combined Use of Oligopeptides, Fragment Libraries, and Natural Compounds: A Comprehensive Approach To Sample the Druggability of Vascular Endothelial Growth Factor.

scientific article published on 10 November 2015

Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2.

scientific article published on 10 April 2013

Computational modeling of the catalytic reaction in triosephosphate isomerase.

scientific article

Conformational response to ligand binding in phosphomannomutase2: insights into inborn glycosylation disorder.

scientific article

Correlated inter-domain motions in adenylate kinase

scientific article (publication date: July 2014)

Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study

scientific article published in July 2004

Determinants and Prediction of Esterase Substrate Promiscuity Patterns.

scientific article published on 28 November 2017

Differential control of heme reactivity in alpha and beta subunits of hemoglobin: a combined Raman spectroscopic and computational study

scientific article published on 14 July 2014

Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding.

scientific article published on 31 August 2015

Direct observation of single DNA structural alterations at low forces with surface-enhanced Raman scattering.

scientific article published on 8 January 2013

Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase

scientific article published in April 2002

Electron transfer in proteins: theory, applications and future perspectives.

scientific article published on October 2013

Electron transfer in the P450cam/PDX complex. The QM/MM e-pathway.

scientific article

Electron transfer pathways in cytochrome c oxidase

scientific article

Exploration of Protein Conformational Change with PELE and Meta-Dynamics

scientific article published on 9 February 2012

Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility

scientific article published on 01 April 2010

Formation of a tyrosine adduct involved in lignin degradation by Trametopsis cervina lignin peroxidase: a novel peroxidase activation mechanism.

scientific article published in June 2013

FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design

scientific article published on 18 February 2020

H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough?

scientific article published on 24 November 2011

Heme electron transfer in peroxidases: the propionate e-pathway

scientific article published on 25 September 2008

Hydrogen bonding pathways in human dihydroorotate dehydrogenase.

scientific article published in October 2006

Identification of dual mTORC1 and mTORC2 inhibitors in melanoma cells: prodigiosin vs. obatoclax.

scientific article

Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach

scientific article published on July 2005

Improving the oxidative stability of a high redox potential fungal peroxidase by rational design

scientific article

In-silico assessment of protein-protein electron transfer. a case study: cytochrome c peroxidase--cytochrome c.

scientific article

Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs.

scientific article published in August 2017

Insights into Laccase Engineering from Molecular Simulations: Toward a Binding-Focused Strategy.

scientific article published on 2 April 2015

Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints

scientific article

Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan

scientific article published on 18 November 2008

Mapping protein electron transfer pathways with QM/MM methods

scientific article published on December 2008

Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases

scientific article published on 4 April 2017

Mechanism of Product Release in NO Detoxification fromMycobacterium tuberculosisTruncated Hemoglobin N

scientific article published in February 2008

Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases

scholarly article

Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery.

scientific article

Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine

scientific article

Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer

scientific article published on October 2005

Molecular interactions of prodiginines with the BH3 domain of anti-apoptotic Bcl-2 family members

scientific article

Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Absolute Binding Free Energy Calculations

scientific article published on 19 December 2013

NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

scientific article published in 2021

New Monte Carlo Based Technique To Study DNA-Ligand Interactions.

scientific article published on 11 November 2015

Nitric oxide reactivity with globins as investigated through computer simulation.

scientific article published on January 2008

PELE web server: atomistic study of biomolecular systems at your fingertips

scientific article

PELE-MSM: A Monte Carlo Based Protocol for the Estimation of Absolute Binding Free Energies

scientific article published on 17 October 2019

PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique.

scientific article

Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450.

scholarly article

Peroxide-dependent formation of a covalent link between Trp51 and the heme in cytochrome c peroxidase.

scientific article

Porphyrin Binding to Gun4 Protein, Facilitated by a Flexible Loop, Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway

scientific article

Predicting Antibody Neutralization Efficacy in Hypermutated Epitopes Using Monte Carlo Simulations

scientific article published on 17 October 2020

Proton-transfer dynamics in the activation of cytochrome P450eryF.

scientific article published in February 2002

Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case

scientific article published on 13 August 2018

Quantum chemical studies of methane monooxygenase: comparision with P450.

scientific article

Raman study of mechanically induced oxygenation state transition of red blood cells using optical tweezers

scientific article published in January 2009

Rational Engineering of Multiple Active Sites in an Ester Hydrolase.

scientific article

Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion

scientific article published on 12 August 2015

Regulation of electron and proton transfer by the protein matrix of cytochrome c oxidase

scientific article

Role of TolC in Klebsiella oxytoca resistance to antibiotics

scientific article published on 24 February 2009

Role of active site histidines in the two half-reactions of the aryl-alcohol oxidase catalytic cycle

scientific article published on 08 August 2012

Simulating Substrate Recognition and Oxidation in Laccases: From Description to Design.

scientific article published on 10 February 2017

Single vs. multiple ligand pathways in globins: a computational view.

scientific article published on 04 February 2013

Solvent Effects on Donor-Acceptor Couplings in Peptides. A Combined QM and MD Study.

scientific article published on December 2009

Stereoselective hydride transfer by aryl-alcohol oxidase, a member of the GMC superfamily

scientific article published on 23 January 2012

Steroid hydroxylation by basidiomycete peroxygenases: a combined experimental and computational study

scientific article published on 10 April 2015

Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi

scientific article

Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase.

scientific article

Synthesis of 1-Naphthol by a Natural Peroxygenase Engineered by Directed Evolution

scientific article published on 17 December 2015

Temperature Effects on Donor-Acceptor Couplings in Peptides. A Combined Quantum Mechanics and Molecular Dynamics Study.

scientific article published in October 2010

The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM study

scientific article published on March 2006

The role of the heme propionates in heme biochemistry.

scientific article

Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder

scientific article

Unveiling prolyl oligopeptidase ligand migration by comprehensive computational techniques.

scientific article published on January 2015

Vibrational resonances and CuB displacement controlled by proton motion in cytochrome c oxidase

scientific article

aquaPELE: A Monte Carlo-Based Algorithm to Sample the Effects of Buried Water Molecules in Proteins

scientific article published on 17 November 2020

pyProCT: Automated Cluster Analysis for Structural Bioinformatics.

scientific article published on 28 July 2014

pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.

scientific article

List of works by Victor Guallar

A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding

A new view of the bacterial cytosol environment

A theoretical multiscale treatment of protein-protein electron transfer: The ferredoxin/ferredoxin-NADP(+) reductase and flavodoxin/ferredoxin-NADP(+) reductase systems

An alternative mechanism for the methylation of phosphoethanolamine catalyzed by Plasmodium falciparum phosphoethanolamine methyltransferase.

An atomistic view on human hemoglobin carbon monoxide migration processes.

Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase.

AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design

Atomic level rendering of DNA-drug encounter.

Atomic picture of ligand migration in toluene 4-monooxygenase

Atomistic simulations shed new light on the activation mechanisms of RORγ and classify it as Type III nuclear hormone receptor regarding ligand-binding paths

Basidiomycete DyPs: Genomic diversity, structural-functional aspects, reaction mechanism and environmental significance

Binding of Thioflavin T and Related Probes to Polymorphic Models of Amyloid-β Fibrils.

Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.

Combined Use of Oligopeptides, Fragment Libraries, and Natural Compounds: A Comprehensive Approach To Sample the Druggability of Vascular Endothelial Growth Factor.

Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2.

Computational modeling of the catalytic reaction in triosephosphate isomerase.

Conformational response to ligand binding in phosphomannomutase2: insights into inborn glycosylation disorder.

Correlated inter-domain motions in adenylate kinase

Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study

Determinants and Prediction of Esterase Substrate Promiscuity Patterns.

Differential control of heme reactivity in alpha and beta subunits of hemoglobin: a combined Raman spectroscopic and computational study

Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding.

Direct observation of single DNA structural alterations at low forces with surface-enhanced Raman scattering.

Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase

Electron transfer in proteins: theory, applications and future perspectives.

Electron transfer in the P450cam/PDX complex. The QM/MM e-pathway.

Electron transfer pathways in cytochrome c oxidase

Exploration of Protein Conformational Change with PELE and Meta-Dynamics

Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility

Formation of a tyrosine adduct involved in lignin degradation by Trametopsis cervina lignin peroxidase: a novel peroxidase activation mechanism.

FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design

H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough?

Heme electron transfer in peroxidases: the propionate e-pathway

Hydrogen bonding pathways in human dihydroorotate dehydrogenase.

Identification of dual mTORC1 and mTORC2 inhibitors in melanoma cells: prodigiosin vs. obatoclax.

Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach

Improving the oxidative stability of a high redox potential fungal peroxidase by rational design

In-silico assessment of protein-protein electron transfer. a case study: cytochrome c peroxidase--cytochrome c.

Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs.

Insights into Laccase Engineering from Molecular Simulations: Toward a Binding-Focused Strategy.

Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints

Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan

Mapping protein electron transfer pathways with QM/MM methods

Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases

Mechanism of Product Release in NO Detoxification fromMycobacterium tuberculosisTruncated Hemoglobin N

Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases

Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery.

Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine

Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer

Molecular interactions of prodiginines with the BH3 domain of anti-apoptotic Bcl-2 family members

Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Absolute Binding Free Energy Calculations

NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

New Monte Carlo Based Technique To Study DNA-Ligand Interactions.

Nitric oxide reactivity with globins as investigated through computer simulation.

PELE web server: atomistic study of biomolecular systems at your fingertips

PELE-MSM: A Monte Carlo Based Protocol for the Estimation of Absolute Binding Free Energies

PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique.

Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450.

Peroxide-dependent formation of a covalent link between Trp51 and the heme in cytochrome c peroxidase.

Porphyrin Binding to Gun4 Protein, Facilitated by a Flexible Loop, Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway

Predicting Antibody Neutralization Efficacy in Hypermutated Epitopes Using Monte Carlo Simulations

Proton-transfer dynamics in the activation of cytochrome P450eryF.

Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case

Quantum chemical studies of methane monooxygenase: comparision with P450.

Raman study of mechanically induced oxygenation state transition of red blood cells using optical tweezers

Rational Engineering of Multiple Active Sites in an Ester Hydrolase.

Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion

Regulation of electron and proton transfer by the protein matrix of cytochrome c oxidase

Role of TolC in Klebsiella oxytoca resistance to antibiotics

Role of active site histidines in the two half-reactions of the aryl-alcohol oxidase catalytic cycle

Simulating Substrate Recognition and Oxidation in Laccases: From Description to Design.

Single vs. multiple ligand pathways in globins: a computational view.

Solvent Effects on Donor-Acceptor Couplings in Peptides. A Combined QM and MD Study.

Stereoselective hydride transfer by aryl-alcohol oxidase, a member of the GMC superfamily

Steroid hydroxylation by basidiomycete peroxygenases: a combined experimental and computational study

Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi

Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase.

Synthesis of 1-Naphthol by a Natural Peroxygenase Engineered by Directed Evolution

Temperature Effects on Donor-Acceptor Couplings in Peptides. A Combined Quantum Mechanics and Molecular Dynamics Study.