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1

K DEEP : Protein-ligand absolute binding affinity prediction via 3D-convolutional neural networks.

Jiménez Luna, José, Skalic, Miha, Martinez-Rosell, Gerard, De Fabritiis, Gianni

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 5.00 MB

english, 2018

2

Discrete random walk models for symmetric Lévy–Feller diffusion processes

Rudolf Gorenflo, Gianni De Fabritiis, Francesco Mainardi

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

1999

Language:

english

File:

PDF, 134 KB

english, 1999

3

HTMD: High-throughput molecular dynamics for molecular discovery

Doerr, Stefan, Harvey, Matthew J., Noé, Frank, De Fabritiis, Gianni

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 1.98 MB

english, 2016

4

Identification of slow molecular order parameters for Markov model construction

Pérez-Hernández, Guillermo, Paul, Fabian, Giorgino, Toni, De Fabritiis, Gianni, Noé, Frank

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.91 MB

english, 2013

5

PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations

Martinez-Rosell, Gerard, Giorgino, Toni, De Fabritiis, Gianni

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 1.94 MB

english, 2017

6

High-throughput automated preparation and simulation of membrane proteins with HTMD

Doerr, Stefan, Giorgino, Toni, Martinez-Rosell, Gerard, Damas, João M., De Fabritiis, Gianni

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 8.92 MB

english, 2017

7

Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

Plattner, Nuria, Doerr, Stefan, De Fabritiis, Gianni, Noé, Frank

Journal:

Nature Chemistry

Year:

2017

Language:

english

File:

PDF, 3.53 MB

english, 2017

8

Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

Herrera-Nieto, Pablo, PÃ©rez, AdriÃ , De Fabritiis, Gianni

Journal:

Scientific Reports

Year:

2020

File:

PDF, 2.06 MB

2020

9

Author Correction: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

Herrera-Nieto, Pablo, PÃ©rez, AdriÃ , De Fabritiis, Gianni

Journal:

Scientific Reports

Year:

2020

File:

PDF, 731 KB

2020

10

Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations

Toni Giorgino, M.J. Harvey, Gianni de Fabritiis

Journal:

Computer Physics Communications

Year:

2010

Language:

english

File:

PDF, 617 KB

english, 2010

11

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

Gianni De Fabritiis, Sebastien Geroult, Peter V. Coveney, Gabriel Waksman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 353 KB

english, 2008

12

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

S. Kashif Sadiq, Gianni De Fabritiis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.18 MB

english, 2010

13

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

Giorgino, Toni, De Fabritiis, Gianni

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 918 KB

english, 2011

14

A survey of computational molecular science using graphics processing units

M. J. Harvey, Gianni De Fabritiis

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2012

Language:

english

File:

PDF, 183 KB

english, 2012

15

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

Matthew J. Harvey, Gianni De Fabritiis

Journal:

Drug Discovery Today

Year:

2012

Language:

english

File:

PDF, 554 KB

english, 2012

16

Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase

Wright, David W., Sadiq, S. Kashif, De Fabritiis, Gianni, Coveney, Peter V.

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.50 MB

english, 2012

17

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

Venken, Tom, Voet, Arnout, De Maeyer, Marc, De Fabritiis, Gianni, Sadiq, S. Kashif

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 253 KB

english, 2013

18

Capturing the Initial Autocatalytic Maturation Mechanism of HIV-1 protease at Atomic Resolution

Sadiq, S. Kashif, De Fabritiis, Gianni

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

19

Membrane lipids are key modulators of the endocannabinoid-hydrolase FAAH

Dainese, Enrico, De Fabritiis, Gianni, Sabatucci, Annalaura, Oddi, Sergio, Angelucci, Clotilde Beatrice, Di Pancrazio, Chiara, Giorgino, Toni, Stanley, Nathaniel, Del Carlo, Michele, Cravatt, Benjamin

Journal:

Biochemical Journal

Year:

2014

Language:

english

File:

PDF, 1.35 MB

english, 2014

20

Computational Modeling of an Epidermal Growth Factor Receptor Single-Mutation Resistance to Cetuximab in Colorectal Cancer Treatment

Buch, Ignasi, Ferruz, Noelia, De Fabritiis, Gianni

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 2.57 MB

english, 2013

21

Optimized Potential of Mean Force Calculations for Standard Binding Free Energies

Buch, Ignasi, Sadiq, S. Kashif, De Fabritiis, Gianni

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 2.53 MB

english, 2011

22

Foundations of dissipative particle dynamics

Flekkøy, Eirik G., Coveney, Peter V., De Fabritiis, Gianni

Journal:

Physical Review E

Year:

2000

Language:

english

File:

PDF, 421 KB

english, 2000

23

Energy controlled insertion of polar molecules in dense fluids

De Fabritiis, Gianni, Delgado-Buscalioni, Rafael, Coveney, Peter V.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 295 KB

english, 2004

24

Kinetic modulation of a disordered protein domain by phosphorylation

Stanley, Nathaniel, Esteban-Martín, Santiago, De Fabritiis, Gianni

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 1.23 MB

english, 2014

25

A COUPLED MOLECULAR-CONTINUUM HYBRID MODEL FOR THE SIMULATION OF MACROMOLECULAR DYNAMICS

GIUPPONI, GIOVANNI, DE FABRITIIS, GIANNI, COVENEY, PETER V.

Journal:

International Journal of Modern Physics C

Year:

2007

Language:

english

File:

PDF, 456 KB

english, 2007

26

Progress in studying intrinsically disordered proteins with atomistic simulations

Stanley, Nathaniel, Esteban-Martín, Santiago, De Fabritiis, Gianni

Journal:

Progress in Biophysics and Molecular Biology

Year:

2015

Language:

english

File:

PDF, 464 KB

english, 2015

27

High throughput molecular dynamics for drug discovery

Stanley, Nathaniel, De Fabritiis, Gianni

Journal:

In Silico Pharmacology

Year:

2015

Language:

english

File:

PDF, 635 KB

english, 2015

28

Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors

Selent, Jana, Sanz, Ferran, Pastor, Manuel, De Fabritiis, Gianni, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 530 KB

english, 2010

29

Spontaneous inward opening of the dopamine transporter is triggered by PIP2-regulated dynamics of the N-terminus

Khelashvili, George, Stanley, Nathaniel, Sahai, Michelle A, Medina, Jaime, LeVine, Michael V, Shi, Lei, de Fabritiis, Gianni, Weinstein, Harel

Journal:

ACS Chemical Neuroscience

Year:

2015

Language:

english

File:

PDF, 20.44 MB

english, 2015

30

Mesoscopic dynamics of Voronoi fluid particles

Serrano, Mar, Fabritiis, Gianni De, Español, Pep, Flekkøy, Eirik G, Coveney, Peter V

Journal:

Journal of Physics A: Mathematical and General Physics

Year:

2002

Language:

english

File:

PDF, 318 KB

english, 2002

31

Insights from Fragment Hit Binding Assays by Molecular Simulations.

Ferruz, Noelia, Harvey, Matthew, Mestres, Jordi, De Fabritiis, Gianni

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 842 KB

english, 2015

32

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

Ignasi Buch, Toni Giorgino and Gianni De Fabritiis

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.24 MB

english, 2011

33

Spontaneous Inward Opening of the Dopamine Transporter is Triggered by PIP2-Regulated Dynamics of the N-Terminus

Khelashvili, George, Stanley, Nathaniel, Sahai, Michelle, Medina, Jaime, LeVine, Michael V., Shi, Lei, De Fabritiis, Gianni, Weinstein, Harel

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 61 KB

english, 2016

34

Binding Kinetics in Drug Discovery

Ferruz, Noelia, De Fabritiis, Gianni

Journal:

Molecular Informatics

Year:

2016

Language:

english

File:

PDF, 2.37 MB

english, 2016

35

Correction to Insights from Fragment Hit Binding Assays by Molecular Simulations

Ferruz, Noelia, Harvey, Matthew J., Mestres, Jordi, De Fabritiis, Gianni

Journal:

Journal of Chemical Information and Modeling

Year:

2016

File:

PDF, 100 KB

2016

36

The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor

Stanley, Nathaniel, Pardo, Leonardo, Fabritiis, Gianni De

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.54 MB

english, 2016

37

Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme

Ferruz, Noelia, Tresadern, Gary, Pineda-Lucena, Antonio, De Fabritiis, Gianni

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.21 MB

english, 2016

38

Simulations meet machine learning in structural biology

Pérez, Adrià, Martínez-Rosell, Gerard, De Fabritiis, Gianni

Journal:

Current Opinion in Structural Biology

Year:

2018

Language:

english

File:

PDF, 600 KB

english, 2018

39

Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors

Martinez-Rosell, Gerard, Harvey, Matt J., De Fabritiis, Gianni

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 6.05 MB

english, 2018

40

LigVoxel: Inpainting binding pockets using 3D-convolutional neural networks

Skalic, Miha, Varela-Rial, Alejandro, Jiménez, José, Martínez-Rosell, Gerard, De Fabritiis, Gianni

Journal:

Year:

2018

Language:

english

File:

PDF, 3.85 MB

english, 2018

41

PlayMolecule BindScope: large scale CNN-based virtual screening on the web

Skalic, Miha, Martínez-Rosell, Gerard, Jiménez, José, De Fabritiis, Gianni, Valencia, Alfonso

Journal:

Year:

2018

Language:

english

File:

PDF, 324 KB

english, 2018

42

PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks

Jiménez, José, Sabbadin, Davide, Cuzzolin, Alberto, Martínez-Rosell, Gerard, Gora, Jacob, Manchester, John, Duca, José, De Fabritiis, Gianni

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 640 KB

english, 2019

43

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

Wang, Jiang, Olsson, Simon, Wehmeyer, Christoph, Pérez, Adrià, Charron, Nicholas E., de Fabritiis, Gianni, Noé, Frank, Clementi, Cecilia

Journal:

ACS Central Science

Year:

2019

Language:

english

File:

PDF, 3.37 MB

english, 2019

44

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

Landin, Erik JB, Lovera, Silvia, de Fabritiis, Gianni, Kelm, Sebastien, Mercier, Joel, MacMillan, David, Sessions, Richard, Taylor, Richard, Sands, Zara A, Joedicke, Lisa, Crump, Matthew Philip

Journal:

Angewandte Chemie International Edition

Year:

2019

Language:

english

File:

PDF, 6.89 MB

english, 2019

45

The Aminotriazole Antagonist Cmpd‐1 Stabilises a Novel Inactive State of the Adenosine 2A Receptor

Landin, Erik JB, Lovera, Silvia, de Fabritiis, Gianni, Kelm, Sebastien, Mercier, Joel, MacMillan, David, Sessions, Richard, Taylor, Richard, Sands, Zara A, Joedicke, Lisa, Crump, Matthew Philip

Journal:

Angewandte Chemie

Year:

2019

Language:

english

File:

PDF, 6.89 MB

english, 2019

46

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

Landin, Erik JB, Lovera, Silvia, de Fabritiis, Gianni, Kelm, Sebastien, Mercier, Joel, MacMillan, David, Sessions, Richard, Taylor, Richard, Sands, Zara A, Joedicke, Lisa, Crump, Matthew Philip

Journal:

Angewandte Chemie International Edition

Year:

2019

File:

PDF, 6.89 MB

2019

47

The Aminotriazole Antagonist Cmpd‐1 Stabilises a Novel Inactive State of the Adenosine 2A Receptor

Landin, Erik JB, Lovera, Silvia, de Fabritiis, Gianni, Kelm, Sebastien, Mercier, Joel, MacMillan, David, Sessions, Richard, Taylor, Richard, Sands, Zara A, Joedicke, Lisa, Crump, Matthew Philip

Journal:

Angewandte Chemie

Year:

2019

File:

PDF, 6.89 MB

2019

48

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

Skalic, Miha, Sabbadin, Davide, Sattarov, Boris, Sciabola, Simone, De Fabritiis, Gianni

Journal:

Molecular Pharmaceutics

Year:

2019

Language:

english

File:

PDF, 8.04 MB

english, 2019

49

Reconstruction of apo A2A receptor activation pathways reveal ligand-competent intermediates and state-dependent cholesterol hotspots

Lovera, Silvia, Cuzzolin, Alberto, Kelm, Sebastian, De Fabritiis, Gianni, Sands, Zara A.

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 1.90 MB

english, 2019

50

DeltaDelta neural networks for lead optimization of small molecule potency

Jiménez-Luna, José, Pérez-Benito, Laura, Martínez-Rosell, Gerard, Sciabola, Simone, Torella, Rubben, Tresadern, Gary, De Fabritiis, Gianni

Journal:

Chemical Science

Year:

2019

File:

PDF, 911 KB

2019

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