List of works - Marco De Vivo

A Binding Site for Nonsteroidal Anti-inflammatory Drugs in Fatty Acid Amide Hydrolase

scientific article

A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases

scientific article published on 9 February 2018

A Transient and Flexible Cation-π Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases

scientific article published on 28 June 2019

A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations

scientific article

A computational study of the binding of propidium to the peripheral anionic site of human acetylcholinesterase.

scientific article

A theoretical DFT investigation of the lysozyme mechanism: computational evidence for a covalent intermediate pathway

scientific article

Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation

scientific article published on 14 September 2018

Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex

scientific article published in 2022

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

scientific article published on 10 August 2017

Anandamide hydrolysis in FAAH reveals a dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion

scientific article published on 3 October 2014

Association Mechanism of Peptide-Coated Metal Nanoparticles with Model Membranes: A Coarse-Grained Study

scientific article published on 03 June 2021

Benzoxazolone carboxamides: potent and systemically active inhibitors of intracellular acid ceramidase.

scientific article published on 13 November 2014

Bridging quantum mechanics and structure-based drug design

scientific article published on January 1, 2011

Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms

scientific article published on 08 May 2020

Catalytic metal ions and enzymatic processing of DNA and RNA.

scientific article

Computational insights into function and inhibition of fatty acid amide hydrolase

scientific article

Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle

scientific article published in August 2005

Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase

scientific article published in January 2007

Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis

scientific article

Correction to "Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation"

scientific article published on 05 June 2019

Covalent inhibitors of fatty acid amide hydrolase: a rationale for the activity of piperidine and piperazine aryl ureas.

scientific article published on 8 September 2011

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

scientific article published on September 2011

Density functional study of the enzymatic reaction catalyzed by a cyclin-dependent kinase

scientific article

Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions

scientific article published on 27 October 2020

Dynamic Origin of Chirality Transfer between Chiral Surface and Achiral Ligand in Au38 Clusters

scientific article published on 14 June 2019

Identification and characterization of carprofen as a multitarget fatty acid amide hydrolase/cyclooxygenase inhibitor

scientific article published on 8 October 2012

Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets

scientific article (publication date: June 2015)

Lid domain plasticity and lipid flexibility modulate enzyme specificity in human monoacylglycerol lipase.

scientific article

Metadynamics as a tool for exploring free energy landscapes of chemical reactions

scientific article

Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations

scientific article published on 27 October 2006

Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase

scientific article published on 9 January 2013

Molecular-Dynamics-Simulation-Directed Rational Design of Nanoreceptors with Targeted Affinity

scientific article published on 02 May 2019

NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles

scientific article published on 25 February 2019

Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site.

scientific article

Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIα.

scientific article published on 8 September 2017

Novel, Potent, and Druglike Tetrahydroquinazoline Inhibitor That Is Highly Selective for Human Topoisomerase II α over β

scientific article published on 20 October 2020

Pharmacophore Hybridization To Discover Novel Topoisomerase II Poisons with Promising Antiproliferative Activity

scientific article

Pharmacophore Identification and Scaffold Exploration to Discover Novel, Potent, and Chemically Stable Inhibitors of Acid Ceramidase in Melanoma Cells.

scientific article

Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism.

scientific article

Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIα and IIβ

scholarly article by Alexandria A Oviatt published in September 2018

Proton shuttles and phosphatase activity in soluble epoxide hydrolase

scientific article published on January 2007

Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5' Structure-Specific Nucleases

scientific article published on 27 January 2020

Role of phosphorylated Thr160 for the activation of the CDK2/Cyclin A complex

scientific article

Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II

scientific article published on 09 September 2019

Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids

scientific article published on 31 July 2019

Synthesis, biological activity, and three-dimensional quantitative structure-activity relationship model for a series of benzo[c]quinolizin-3-ones, nonsteroidal inhibitors of human steroid 5alpha-reductase 1.

scientific article published in July 2004

The increasing role of QM/MM in drug discovery.

scientific article published on January 2012

Theoretical Insights into the Mechanism of Carbon Monoxide (CO) Release from CO-Releasing Molecules

scientific article published on 22 June 2012

Understanding the effect of magnesium ion concentration on the catalytic activity of ribonuclease H through computation: does a third metal binding site modulate endonuclease catalysis?

scientific article published on October 2010

Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation

scientific article published on June 2009

Visualizing group II intron dynamics between the first and second steps of splicing

scientific article published on 05 June 2020

Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis

scientific article published on 15 January 2013

List of works by Marco De Vivo

A Binding Site for Nonsteroidal Anti-inflammatory Drugs in Fatty Acid Amide Hydrolase

A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases

A Transient and Flexible Cation-π Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases

A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations

A computational study of the binding of propidium to the peripheral anionic site of human acetylcholinesterase.

A theoretical DFT investigation of the lysozyme mechanism: computational evidence for a covalent intermediate pathway

Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation

Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

Anandamide hydrolysis in FAAH reveals a dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion

Association Mechanism of Peptide-Coated Metal Nanoparticles with Model Membranes: A Coarse-Grained Study

Benzoxazolone carboxamides: potent and systemically active inhibitors of intracellular acid ceramidase.

Bridging quantum mechanics and structure-based drug design

Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms

Catalytic metal ions and enzymatic processing of DNA and RNA.

Computational insights into function and inhibition of fatty acid amide hydrolase

Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle

Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase

Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis

Correction to "Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation"

Covalent inhibitors of fatty acid amide hydrolase: a rationale for the activity of piperidine and piperazine aryl ureas.

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

Density functional study of the enzymatic reaction catalyzed by a cyclin-dependent kinase

Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions

Dynamic Origin of Chirality Transfer between Chiral Surface and Achiral Ligand in Au38 Clusters

Identification and characterization of carprofen as a multitarget fatty acid amide hydrolase/cyclooxygenase inhibitor

Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets

Lid domain plasticity and lipid flexibility modulate enzyme specificity in human monoacylglycerol lipase.

Metadynamics as a tool for exploring free energy landscapes of chemical reactions

Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations

Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase

Molecular-Dynamics-Simulation-Directed Rational Design of Nanoreceptors with Targeted Affinity

NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles

Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site.

Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIα.

Novel, Potent, and Druglike Tetrahydroquinazoline Inhibitor That Is Highly Selective for Human Topoisomerase II α over β

Pharmacophore Hybridization To Discover Novel Topoisomerase II Poisons with Promising Antiproliferative Activity

Pharmacophore Identification and Scaffold Exploration to Discover Novel, Potent, and Chemically Stable Inhibitors of Acid Ceramidase in Melanoma Cells.

Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism.

Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIα and IIβ

Proton shuttles and phosphatase activity in soluble epoxide hydrolase

Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5' Structure-Specific Nucleases

Role of phosphorylated Thr160 for the activation of the CDK2/Cyclin A complex

Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II

Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids

Synthesis, biological activity, and three-dimensional quantitative structure-activity relationship model for a series of benzo[c]quinolizin-3-ones, nonsteroidal inhibitors of human steroid 5alpha-reductase 1.

The increasing role of QM/MM in drug discovery.

Theoretical Insights into the Mechanism of Carbon Monoxide (CO) Release from CO-Releasing Molecules

Understanding the effect of magnesium ion concentration on the catalytic activity of ribonuclease H through computation: does a third metal binding site modulate endonuclease catalysis?

Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation

Visualizing group II intron dynamics between the first and second steps of splicing

Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis