Lista de obras - Francesco Luigi Gervasio

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

artículo científico publicado en 2016

A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions

artículo científico publicado en 2011

A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics

A Simple Mechanism Underlying the Effect of Protecting Osmolytes on Protein Folding.

artículo científico publicado en 2011

A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors

artículo científico publicado en 2016

A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors

article published in 2016

A Variational Definition of Electrostatic Potential Derived Charges

A combined activation mechanism for the glucagon receptor

artículo científico publicado en 2020

A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.

artículo científico publicado en 2004

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

artículo científico publicado en 2016

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands

artículo científico publicado en 2017

Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation

artículo científico publicado en 2023

Assessing the Accuracy of Metadynamics†

scientific article published on 01 April 2005

Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors

article

Assessment of the model refinement category in CASP12.

artículo científico publicado en 2017

Backbone assignment of the tyrosine kinase Src catalytic domain in complex with imatinib

artículo científico publicado en 2011

Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase

artículo científico publicado en 2016

Bifunctional catalysis by natural cinchona alkaloids: a mechanism explained.

artículo científico publicado en 2009

BioSimSpace: An interoperable Python framework for biomolecular simulation

scientific article published on 22 November 2019

Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece

artículo científico publicado en 2011

Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

artículo científico publicado en 2016

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

artículo científico publicado en 2017

Charge Localization in DNA Fibers

scientific article published in Physical Review Letters

Charge localization in stacked radical cation DNA base pairs and the benzene dimer studied by self-interaction corrected density-functional theory

artículo científico publicado en 2007

Charge transfer mechanism in a PolydGpdCp fiber and in wet DNA

Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin

article

Conformational Changes and Free Energies in a Proline Isomerase

Conformational Distribution of Gas-phase Glycerol

Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase

artículo científico publicado en 2016

Conformational Selection versus Induced Fit in Kinases: The Case of PI3K‐γ ⬇️

artículo científico publicado el 16 de enero de 2012

Conformational changes and gating at the selectivity filter of potassium channels.

artículo científico publicado en 2008

Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET.

artículo científico publicado en 2017

Cyclin-dependent kinases: bridging their structure and function through computations.

artículo científico publicado en 2011

DFT modeling of biological systems

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

artículo científico publicado en 2016

Defining an Optimal Metric for the Path Collective Variables

scientific article published on 05 December 2018

Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance

scientific article published in Scientific Reports

Density Functional Calculation of Structural and Vibrational Properties of Glycerol

article

Determination of the Potential of Mean Force of Aromatic Amino Acid Complexes in Various Solvents Using Molecular Dynamics Simulations: The Case of the Tryptophan−Histidine Pair

article

Double Proton Coupled Charge Transfer in DNA

artículo científico publicado en 2006

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase ⬇️

artículo científico publicado el 10 de junio de 2013

Efficient Numerical Reconstruction of Protein Folding Kinetics with Partial Path Sampling and Pathlike Variables

scientific article published in Physical Review Letters

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

artículo científico publicado en 2006

Electronic structure of wet DNA.

artículo científico publicado en 2002

Enabling multiscale modeling in systems medicine

artículo científico publicado en 2014

Exploring Cryptic Pockets Formation in Targets of Pharmaceutical Interest with SWISH

artículo científico publicado en 2018

Exploring complex protein-ligand recognition mechanisms with coarse metadynamics

artículo científico publicado en 2009

Exploring the gating mechanism in the ClC chloride channel via metadynamics

artículo científico publicado en 2006

Flexible docking in solution using metadynamics

artículo científico publicado en 2005

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics

artículo científico publicado en 2006

Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors.

artículo científico publicado en 2010

From A to B in free energy space

artículo científico publicado en 2007

From residue coevolution to protein conformational ensembles and functional dynamics

artículo científico publicado en 2015

Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor

article

Influence of DNA structure on the reactivity of the guanine radical cation

artículo científico publicado en 2004

Inhibition of tumor angiogenesis and growth by a small-molecule multi-FGF receptor blocker with allosteric properties

artículo científico publicado en 2013

Insight into the folding inhibition of the HIV-1 protease by a small peptide

artículo científico publicado en 2007

Inter-residue and solvent-residue interactions in proteins: a statistical study on experimental structures

artículo científico publicado en 2004

Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases

artículo científico publicado en 2018

Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

artículo científico publicado en 2020

Investigating allosteric effects on the functional dynamics of β2-adrenergic ternary complexes with enhanced-sampling simulations

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

artículo científico publicado en 2007

Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms

artículo científico publicado en 2014

Is the T-Shaped Toluene Dimer a Stable Intermolecular Complex?

Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding

artículo científico publicado en 2006

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases

artículo científico publicado en 2016

Modulating Ligand Dissociation through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers

scientific article published on 14 November 2019

Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

artículo científico publicado en 2010

Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus

artículo científico publicado en 2011

Molecular engineering of polymersome surface topology

artículo científico publicado en 2016

Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling

artículo científico publicado en 2013

Multiple routes and milestones in the folding of HIV-1 protease monomer

artículo científico publicado en 2010

New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations

artículo científico publicado en 2015

New advances in metadynamics

New insights in protein kinase conformational dynamics

artículo científico

Non-specific protein-DNA interactions control I-CreI target binding and cleavage

artículo científico publicado en 2012

Phosphatidylinositol 4,5-bisphosphate triggers activation of focal adhesion kinase by inducing clustering and conformational changes

artículo científico publicado en 2014

Protein CoAlation and antioxidant function of Coenzyme A in prokaryotic cells

artículo científico publicado en 2018

Protein Conformational Plasticity: the “off-on” Switching Movement in Cdk5

article by Andrea Cavalli et al published 2007 in AIP Conference Proceedings

Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

scientific article published on 01 January 2009

Role of glutamine synthetase in angiogenesis beyond glutamine synthesis ⬇️

artículo científico publicado en 2018

Solvent Effects on Charge Spatial Extent in DNA and Implications for Transfer

artículo científico publicado en 2007

Stacking and T-shape competition in aromatic-aromatic amino acid interactions

artículo científico publicado en 2002

Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer

artículo científico publicado en 2019

The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation

scientific article published on 30 January 2012

The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study ⬇️

artículo científico publicado en 2015

The Role of Post-translational Modifications on the Energy Landscape of Huntingtin N-Terminus

scientific article published on 01 October 2019

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

artículo científico publicado en 2016

The SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motion

artículo científico publicado en 2014

The architecture of EGFR's basal complexes reveals autoinhibition mechanisms in dimers and oligomers

artículo científico publicado en 2018

The effect of a widespread cancer-causing mutation on the inactive to active dynamics of the B-Raf kinase

artículo científico publicado en 2015

The mechanism of allosteric coupling in choline kinase α1 revealed by the action of a rationally designed inhibitor

artículo científico publicado en 2013

The nature of intermolecular interactions between aromatic amino acid residues

artículo científico publicado en 2002

The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge

The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge

artículo científico publicado en 2005

The structure of the Pro-domain of mouse proNGF in contact with the NGF domain

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin

artículo científico publicado en 2008

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics

artículo científico publicado en 2015

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations

artículo científico publicado en 2016

Understanding Ligand Binding Selectivity in a Prototypical GPCR Family

artículo científico publicado en 2019

Using metadynamics and path collective variables to study ligand binding and induced conformational transitions

artículo científico publicado en 2012

Lista de obras de Francesco Luigi Gervasio

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions

A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics

A Simple Mechanism Underlying the Effect of Protecting Osmolytes on Protein Folding.

A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors

A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors

A Variational Definition of Electrostatic Potential Derived Charges

A combined activation mechanism for the glucagon receptor

A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands

Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation

Assessing the Accuracy of Metadynamics†

Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors

Assessment of the model refinement category in CASP12.

Backbone assignment of the tyrosine kinase Src catalytic domain in complex with imatinib

Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase

Bifunctional catalysis by natural cinchona alkaloids: a mechanism explained.

BioSimSpace: An interoperable Python framework for biomolecular simulation

Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece

Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

Charge Localization in DNA Fibers

Charge localization in stacked radical cation DNA base pairs and the benzene dimer studied by self-interaction corrected density-functional theory

Charge transfer mechanism in a PolydGpdCp fiber and in wet DNA

Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin

Conformational Changes and Free Energies in a Proline Isomerase

Conformational Distribution of Gas-phase Glycerol

Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase

Conformational Selection versus Induced Fit in Kinases: The Case of PI3K‐γ ⬇️

Conformational changes and gating at the selectivity filter of potassium channels.

Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET.

Cyclin-dependent kinases: bridging their structure and function through computations.

DFT modeling of biological systems

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

Defining an Optimal Metric for the Path Collective Variables

Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance

Density Functional Calculation of Structural and Vibrational Properties of Glycerol

Determination of the Potential of Mean Force of Aromatic Amino Acid Complexes in Various Solvents Using Molecular Dynamics Simulations: The Case of the Tryptophan−Histidine Pair

Double Proton Coupled Charge Transfer in DNA

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase ⬇️

Efficient Numerical Reconstruction of Protein Folding Kinetics with Partial Path Sampling and Pathlike Variables

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

Electronic structure of wet DNA.

Enabling multiscale modeling in systems medicine

Exploring Cryptic Pockets Formation in Targets of Pharmaceutical Interest with SWISH

Exploring complex protein-ligand recognition mechanisms with coarse metadynamics

Exploring the gating mechanism in the ClC chloride channel via metadynamics

Flexible docking in solution using metadynamics

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics

Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors.

From A to B in free energy space

From residue coevolution to protein conformational ensembles and functional dynamics

Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor

Influence of DNA structure on the reactivity of the guanine radical cation

Inhibition of tumor angiogenesis and growth by a small-molecule multi-FGF receptor blocker with allosteric properties

Insight into the folding inhibition of the HIV-1 protease by a small peptide

Inter-residue and solvent-residue interactions in proteins: a statistical study on experimental structures

Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases

Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

Investigating allosteric effects on the functional dynamics of β2-adrenergic ternary complexes with enhanced-sampling simulations

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms

Is the T-Shaped Toluene Dimer a Stable Intermolecular Complex?

Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases

Modulating Ligand Dissociation through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers

Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus

Molecular engineering of polymersome surface topology

Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling

Multiple routes and milestones in the folding of HIV-1 protease monomer

New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations

New advances in metadynamics

New insights in protein kinase conformational dynamics

Non-specific protein-DNA interactions control I-CreI target binding and cleavage

Phosphatidylinositol 4,5-bisphosphate triggers activation of focal adhesion kinase by inducing clustering and conformational changes