List of works - Gianni de Fabritiis

A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A.

scientific article published on 06 May 2011

A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning

scientific article published on 08 August 2019

Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation.

scientific article

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware.

scientific article published in September 2009

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

scientific article

Computational modeling of an epidermal growth factor receptor single-mutation resistance to cetuximab in colorectal cancer treatment.

scientific article published on 18 November 2013

DeltaDelta neural networks for lead optimization of small molecule potency

scientific article published on 16 October 2019

Detection of new biased agonists for the serotonin 5-HT2A receptor: modeling and experimental validation.

scientific article published on 6 February 2015

Embedding molecular dynamics within fluctuating hydrodynamics in multiscale simulations of liquids

scientific article published on 25 September 2007

Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics.

scientific article

Energy controlled insertion of polar molecules in dense fluids

scientific article published on 01 December 2004

Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing.

scientific article published on November 2010

Fluctuating hydrodynamic modeling of fluids at the nanoscale.

scientific article published on 8 February 2007

Foundations of dissipative particle dynamics

scientific article published on 01 August 2000

From Target to Drug: Generative Modeling for the Multimodal Structure-Based Ligand Design

scientific article published on 10 September 2019

GPCRmd uncovers the dynamics of the 3D-GPCRome

scientific article published on 13 July 2020

Generative Models for Molecular Design

scientific article published on 01 December 2020

High throughput molecular dynamics for drug discovery.

scientific article published on 13 February 2015

High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD.

scientific article published on 19 July 2017

High-throughput all-atom molecular dynamics simulations using distributed computing.

scientific article published on March 2010

High-throughput molecular dynamics: the powerful new tool for drug discovery ⬇️

scientific article published on 05 April 2012

Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules.

scientific article published in April 2007

Induced effects of sodium ions on dopaminergic G-protein coupled receptors

scientific article

Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain

scientific article published in September 2008

Integrative Biology — the challenges of developing a collaborative research environment for heart and cancer modelling

article published in 2007

Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations

scientific article published on 30 January 2014

Kinetic modulation of a disordered protein domain by phosphorylation

scientific article published on 28 October 2014

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

scientific article published on 15 April 2019

Membrane lipids are key modulators of the endocannabinoid-hydrolase FAAH.

scientific article published on February 2014

Membrane-sensitive conformational states of helix 8 in the metabotropic Glu2 receptor, a class C GPCR

scientific article (publication date: 2012)

Multiscale modeling of liquids with molecular specificity

scientific article published on 25 September 2006

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations.

scientific article published on 4 April 2014

Optimized Potential of Mean Force Calculations for Standard Binding Free Energies.

scientific article published on 11 May 2011

PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks

scientific article published on 10 January 2019

PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations

scientific article published on 01 April 2020

Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome

scientific article published on 23 July 2020

Rapid Conformational Fluctuations of Disordered HIV-1 Fusion Peptide in Solution.

scientific article

Shape-Based Generative Modeling for de Novo Drug Design

scientific article published on 28 February 2019

Statistical analysis of global connectivity and activity distributions in cellular networks.

scientific article published in July 2010

The Aminotriazole Antagonist Cmpd-1 Stabilises a Distinct Inactive State of the Adenosine 2A Receptor

scientific article published on 05 June 2019

Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase.

scientific article published on 30 July 2012

TorchMD: A Deep Learning Framework for Molecular Simulations

scientific article published on 17 March 2021

Understanding molecular recognition by kinetic network models constructed from molecular dynamics simulations

scientific article published on January 2014

Visualizing the Induced Binding of SH2-Phosphopeptide

scientific article published on 15 March 2012

List of works by Gianni de Fabritiis

A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A.

A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning

Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation.

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware.

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

Computational modeling of an epidermal growth factor receptor single-mutation resistance to cetuximab in colorectal cancer treatment.

DeltaDelta neural networks for lead optimization of small molecule potency

Detection of new biased agonists for the serotonin 5-HT2A receptor: modeling and experimental validation.

Embedding molecular dynamics within fluctuating hydrodynamics in multiscale simulations of liquids

Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics.

Energy controlled insertion of polar molecules in dense fluids

Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing.

Fluctuating hydrodynamic modeling of fluids at the nanoscale.

Foundations of dissipative particle dynamics

From Target to Drug: Generative Modeling for the Multimodal Structure-Based Ligand Design

GPCRmd uncovers the dynamics of the 3D-GPCRome

Generative Models for Molecular Design

High throughput molecular dynamics for drug discovery.

High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD.

High-throughput all-atom molecular dynamics simulations using distributed computing.

High-throughput molecular dynamics: the powerful new tool for drug discovery ⬇️

Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules.

Induced effects of sodium ions on dopaminergic G-protein coupled receptors

Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain

Integrative Biology — the challenges of developing a collaborative research environment for heart and cancer modelling

Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations

Kinetic modulation of a disordered protein domain by phosphorylation

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

Membrane lipids are key modulators of the endocannabinoid-hydrolase FAAH.

Membrane-sensitive conformational states of helix 8 in the metabotropic Glu2 receptor, a class C GPCR

Multiscale modeling of liquids with molecular specificity

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations.

Optimized Potential of Mean Force Calculations for Standard Binding Free Energies.

PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks

PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations

Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome

Rapid Conformational Fluctuations of Disordered HIV-1 Fusion Peptide in Solution.

Shape-Based Generative Modeling for de Novo Drug Design

Statistical analysis of global connectivity and activity distributions in cellular networks.

The Aminotriazole Antagonist Cmpd-1 Stabilises a Distinct Inactive State of the Adenosine 2A Receptor

Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase.

TorchMD: A Deep Learning Framework for Molecular Simulations

Understanding molecular recognition by kinetic network models constructed from molecular dynamics simulations

Visualizing the Induced Binding of SH2-Phosphopeptide