Lista de obras -

2016 update on APBioNet's annual international conference on bioinformatics (InCoB)

artículo científico publicado en 2016

A Funneled Conformational Landscape Governs Flavivirus Fusion Peptide Interaction with Lipid Membranes.

artículo científico publicado en 2018

A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone

artículo científico publicado en 2017

A T164S mutation in the dengue virus NS1 protein is associated with greater disease severity in mice

scientific article published on 01 June 2019

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

scientific article published on 17 May 2018

A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4.

artículo científico publicado en 2017

A study on Fe(2+) - α-helical-rich keratin complex formation using isothermal titration calorimetry and molecular dynamics simulation.

artículo científico publicado en 2014

A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles

artículo científico publicado en 2012

Activation of Toll-like receptors nucleates assembly of the MyDDosome signaling hub.

artículo científico publicado en 2018

Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism.

artículo científico publicado en 2017

An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit

artículo científico publicado en 2020

An Optical Technique for Mapping Microviscosity Dynamics in Cellular Organelles

artículo científico publicado en 2018

Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations.

artículo científico publicado en 2010

Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.

artículo científico publicado en 2007

Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

artículo científico publicado en 2016

Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment

artículo científico publicado en 2016

Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.

artículo científico publicado en 2009

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

artículo científico publicado en 2008

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

scientific article published on 20 October 2006

Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer.

artículo científico publicado en 2008

Concentration- and pH-Dependent Oligomerization of the Thrombin-Derived C-Terminal Peptide TCP-25

artículo científico publicado en 2020

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

artículo científico publicado en 2004

Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component.

artículo científico publicado en 2006

Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes

artículo científico publicado en 2013

Directing GDNF-mediated neuronal signaling with proactively programmable cell-surface saccharide-free glycosaminoglycan mimetics

scientific article published on 01 January 2019

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

artículo científico publicado en 2016

Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.

artículo científico publicado en 2013

Editorial

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

artículo científico publicado en 2014

Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway

scientific article published on 09 January 2019

Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

artículo científico publicado en 2016

Energetics of Endotoxin Recognition in the Toll-Like Receptor 4 Innate Immune Response

artículo científico publicado en 2015

Engineering an Osmosensor by Pivotal Histidine Positioning within Disordered Helices

scientific article published on 29 November 2018

Evidence that TLR4 Is Not a Receptor for Saturated Fatty Acids but Mediates Lipid-Induced Inflammation by Reprogramming Macrophage Metabolism.

artículo científico publicado en 2018

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study ⬇️

artículo científico publicado el 24 de febrero de 2011

Extending the Martini Coarse-Grained Force Field to N-Glycans

scientific article published on 23 July 2020

Facile saccharide-free mimetics that recapitulate key features of glycosaminoglycan sulfation patterns

scientific article published on 24 August 2018

Flavivirus Cross-Reactivity to Dengue Nonstructural Protein 1 Antigen Detection Assays

artículo científico publicado en 2019

Free energy predictions of ligand binding to an α-helix using steered molecular dynamics and umbrella sampling simulations

scientific article published on 17 July 2014

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

artículo científico publicado en 2016

Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States

artículo científico publicado en 2017

Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization.

artículo científico publicado en 2008

How Ligand Binding Affects the Dynamical Transition Temperature in Proteins

scientific article published on 03 March 2020

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria

artículo científico publicado en 2016

Impairing Cohesin Smc1/3 Head Engagement Compensates for the Lack of Eco1 Function.

artículo científico publicado en 2016

Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1.

artículo científico publicado en 2012

Infectivity of Dengue Virus Serotypes 1 and 2 Is Correlated with E-Protein Intrinsic Dynamics but Not to Envelope Conformations

artículo científico publicado en 2019

Influence of pH on the activity of thrombin-derived antimicrobial peptides

artículo científico publicado en 2018

Insertion and assembly of membrane proteins via simulation.

artículo científico publicado en 2006

Insights into water accessible pathways and the inactivation mechanism of proton translocation by the membrane-embedded domain of V-type ATPases

artículo científico publicado en 2019

Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study

artículo científico publicado en 2015

Introductory note for JBCB special issue

artículo científico publicado en 2016

Ion channel gating: insights via molecular simulations.

artículo científico publicado en 2003

Linker length affects photostability of protein-targeted sensor of cellular microviscosity

artículo científico publicado en 2019

Lipid/protein interactions and the membrane/water interfacial region

scientific article published on 01 December 2003

MD simulations of spontaneous membrane protein/detergent micelle formation.

artículo científico publicado en 2004

Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody

artículo científico publicado en 2018

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.

artículo científico publicado en 2003

Membrane protein structure quality in molecular dynamics simulation.

artículo científico publicado en 2005

Membrane recognition and dynamics of the RNA degradosome

artículo científico publicado en 2015

Minor pseudopilin self-assembly primes type II secretion pseudopilus elongation.

artículo científico publicado en 2012

Molecular basis for the maintenance of lipid asymmetry in the outer membrane ofEscherichia coli

Molecular basis of dengue virus serotype 2 morphological switch from 29°C to 37°C

artículo científico publicado en 2019

Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment.

artículo científico publicado en 2012

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation

artículo científico publicado en 2011

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment

scientific article published on 01 January 2005

Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

artículo científico publicado en 2020

Molecular dynamics simulations of membrane proteins

artículo científico publicado en 2008

Molecular dynamics simulations of membrane proteins

artículo científico publicado en 2015

Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.

artículo científico publicado en 2011

Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein

scientific article published on 15 October 2020

Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions

scientific article published on 01 January 2019

Multiscale modeling of innate immune receptors: Endotoxin recognition and regulation by host defense peptides

artículo científico publicado en 2019

Multiscale modelling and simulation of viruses

scientific article published on 25 January 2020

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses

artículo científico publicado en 2016

Multiscale molecular dynamics simulations of membrane proteins.

artículo científico

Not all therapeutic antibody isotypes are equal: the case of IgM versus IgG in Pertuzumab and Trastuzumab

scientific article published on 12 February 2020

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment.

artículo científico publicado en 2016

On the ion coupling mechanism of the MATE transporter ClbM

scientific article published on 28 November 2019

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.

artículo científico publicado en 2007

Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble

artículo científico publicado en 2018

Polar N-terminal Residues Conserved in Type 2 Secretion Pseudopilins Determine Subunit Targeting and Membrane Extraction Steps during Fibre Assembly

artículo científico publicado en 2017

Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens.

artículo científico publicado en 2009

Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes

artículo científico publicado en 2017

Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold.

artículo científico publicado en 2017

Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations

artículo científico publicado en 2016

Revisiting the interaction between the chaperone Skp and lipopolysaccharide

artículo científico publicado en 2015

Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification

artículo científico publicado en 2013

Selective inhibitors of trypanosomal uridylyl transferase RET1 establish druggability of RNA post-transcriptional modifications

artículo científico publicado en 2016

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.

artículo científico publicado en 2008

Single mutations in the ε subunit from thermophilic PS3 generate a high binding affinity site for ATP

artículo científico publicado en 2018

Single-molecule studies of flavivirus envelope dynamics: Experiment and computation

artículo científico publicado en 2018

Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis

artículo científico publicado en 2016

Structural and energetic basis for H+ versus Na+ binding selectivity in ATP synthase Fo rotors

artículo científico publicado en 2010

Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides

artículo científico publicado en 2018

Structural basis for endotoxin neutralization and anti-inflammatory activity of thrombin-derived C-terminal peptides

Structure and subunit arrangement of Mycobacterial F1FO ATP synthase and novel features of the unique mycobacterial subunit δ

artículo científico publicado en 2019

Structure mapping of dengue and Zika viruses reveals functional long-range interactions

scientific article published on 29 March 2019

Structure mapping of dengue and Zika viruses reveals new functional long-range interactions

scholarly article published 1 August 2018

Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses

artículo científico publicado en 2016

The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain

artículo científico publicado en 2015

The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity.

artículo científico publicado en 2015

The architecture of the OmpC-MlaA complex sheds light on the maintenance of outer membrane lipid asymmetry in

artículo científico publicado en 2018

The disordered plant dehydrin Lti30 protects the membrane during water-related stress by cross-linking lipids

scientific article published on 28 February 2019

The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule

artículo científico publicado en 2012

The role of protein-protein interactions in Toll-like receptor function.

artículo científico

The severity of hereditary porphyria is modulated by the porphyrin exporter and Lan antigen ABCB6.

artículo científico publicado en 2016

The simulation approach to bacterial outer membrane proteins.

artículo científico publicado en 2004

The simulation approach to lipid-protein interactions

artículo científico publicado en 2013

The structural basis for endotoxin-induced allosteric regulation of the Toll-like receptor 4 (TLR4) innate immune receptor.

scientific article published on 30 October 2013

The structural basis for membrane assembly of immunoreceptor signalling complexes

scientific article published on 27 August 2019

Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer

artículo científico publicado en 2006

Understanding dengue virus capsid protein disordered N-Terminus and pep14-23-based inhibition

artículo científico publicado en 2014

Lista de obras de

2016 update on APBioNet's annual international conference on bioinformatics (InCoB)

A Funneled Conformational Landscape Governs Flavivirus Fusion Peptide Interaction with Lipid Membranes.

A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone

A T164S mutation in the dengue virus NS1 protein is associated with greater disease severity in mice

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4.

A study on Fe(2+) - α-helical-rich keratin complex formation using isothermal titration calorimetry and molecular dynamics simulation.

A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles

Activation of Toll-like receptors nucleates assembly of the MyDDosome signaling hub.

Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism.

An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit

An Optical Technique for Mapping Microviscosity Dynamics in Cellular Organelles

Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations.

Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.

Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment

Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer.

Concentration- and pH-Dependent Oligomerization of the Thrombin-Derived C-Terminal Peptide TCP-25

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component.

Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes

Directing GDNF-mediated neuronal signaling with proactively programmable cell-surface saccharide-free glycosaminoglycan mimetics

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.

Editorial

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway

Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

Energetics of Endotoxin Recognition in the Toll-Like Receptor 4 Innate Immune Response

Engineering an Osmosensor by Pivotal Histidine Positioning within Disordered Helices

Evidence that TLR4 Is Not a Receptor for Saturated Fatty Acids but Mediates Lipid-Induced Inflammation by Reprogramming Macrophage Metabolism.

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study ⬇️

Extending the Martini Coarse-Grained Force Field to N-Glycans

Facile saccharide-free mimetics that recapitulate key features of glycosaminoglycan sulfation patterns

Flavivirus Cross-Reactivity to Dengue Nonstructural Protein 1 Antigen Detection Assays

Free energy predictions of ligand binding to an α-helix using steered molecular dynamics and umbrella sampling simulations

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States

Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization.

How Ligand Binding Affects the Dynamical Transition Temperature in Proteins

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria

Impairing Cohesin Smc1/3 Head Engagement Compensates for the Lack of Eco1 Function.

Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1.

Infectivity of Dengue Virus Serotypes 1 and 2 Is Correlated with E-Protein Intrinsic Dynamics but Not to Envelope Conformations

Influence of pH on the activity of thrombin-derived antimicrobial peptides

Insertion and assembly of membrane proteins via simulation.

Insights into water accessible pathways and the inactivation mechanism of proton translocation by the membrane-embedded domain of V-type ATPases

Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study

Introductory note for JBCB special issue

Ion channel gating: insights via molecular simulations.

Linker length affects photostability of protein-targeted sensor of cellular microviscosity

Lipid/protein interactions and the membrane/water interfacial region

MD simulations of spontaneous membrane protein/detergent micelle formation.

Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.

Membrane protein structure quality in molecular dynamics simulation.

Membrane recognition and dynamics of the RNA degradosome

Minor pseudopilin self-assembly primes type II secretion pseudopilus elongation.

Molecular basis for the maintenance of lipid asymmetry in the outer membrane ofEscherichia coli

Molecular basis of dengue virus serotype 2 morphological switch from 29°C to 37°C

Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment.

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment

Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

Molecular dynamics simulations of membrane proteins

Molecular dynamics simulations of membrane proteins

Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.

Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein

Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions

Multiscale modeling of innate immune receptors: Endotoxin recognition and regulation by host defense peptides

Multiscale modelling and simulation of viruses

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses

Multiscale molecular dynamics simulations of membrane proteins.

Not all therapeutic antibody isotypes are equal: the case of IgM versus IgG in Pertuzumab and Trastuzumab

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment.

On the ion coupling mechanism of the MATE transporter ClbM