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Science

Since 2006, Acellera supports applied research for the development of biomedical simulation methods and machine learning predictors via agreements with academic institutions.

Furthermore, we create new software and hardware infrastructure for performing biomolecular simulations in high-throughput. Salient examples are ACEMD, HTMD or Metrocubo.

We would be happy to consider scientific collaborations with interested parties to demonstrate the potential of biomolecular simulations and deep learning. We are open to research projects (e.g. European projects) as well as other collaboration formats. Do not hesitate to contact us today.


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Science

Publications

Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series

Sabanés Zariquiey, Francesc; Pérez, Adrià; Majewski, Maciej; Gallicchio, Emilio; De Fabritiis, Gianni

Journal of Chemical Information and Modeling

2023

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Applications

NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics

Galvelis, Raimondas; Varela-Rial, Alejandro; Doerr, Stefan; Fino, Roberto; Eastman, Peter; Markland, Thomas E; Chodera, John D; De Fabritiis, Gianni

arXiv preprint arXiv:2201.08110

2022

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ACEMD/HTMD/AceCloud

TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials

Thölke, Philipp; De Fabritiis, Gianni

International Conference on Learning Representations

2022

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Applications

Machine Learning Coarse-Grained Potentials of Protein Thermodynamics

Majewski, Maciej; Pérez, Adrià; Thölke, Philipp; Doerr, Stefan; Charron, Nicholas E; Giorgino, Toni; Husic, Brooke E; Clementi, Cecilia; Noé, Frank; De Fabritiis, Gianni

arXiv preprint arXiv:2212.07492

2022

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Applications

PlayMolecule glimpse: Understanding protein–ligand property predictions with interpretable neural networks

Varela-Rial, Alejandro; Maryanow, Iain; Majewski, Maciej; Doerr, Stefan; Schapin, Nikolai; Jiménez-Luna, José; De Fabritiis, Gianni

Journal of chemical information and modeling

2022

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Applications

Structure based virtual screening: Fast and slow

Varela‐Rial, Alejandro; Majewski, Maciej; De Fabritiis, Gianni

Wiley Interdisciplinary Reviews: Computational Molecular Science

2022

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Protein-Ligand Binding

TorchMD: A deep learning framework for molecular simulations

Doerr, Stefan; Majewski, Maciej; Pérez, Adrià; Kramer, Andreas; Clementi, Cecilia; Noe, Frank; Giorgino, Toni; De Fabritiis, Gianni

Journal of chemical theory and computation

2021

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Applications

PlayMolecule CrypticScout: predicting protein cryptic sites using mixed-solvent molecular simulations

Martinez-Rosell, Gerard; Lovera, Silvia; Sands, Zara A; De Fabritiis, Gianni

Journal of Chemical Information and Modeling

2020

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Applications

SkeleDock: a web application for scaffold docking in PlayMolecule

Varela-Rial, Alejandro; Majewski, Maciej; Cuzzolin, Alberto; Martínez-Rosell, Gerard; De Fabritiis, Gianni

Journal of Chemical Information and Modeling

2020

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Applications

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

Herrera-Nieto, Pablo; Pérez, Adrià; De Fabritiis, Gianni

Scientific reports

2020

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Applications

Small molecule modulation of intrinsically disordered proteins using molecular dynamics simulations

Herrera-Nieto, Pablo; Pérez, Adrià; De Fabritiis, Gianni

Journal of Chemical Information and Modeling

2020

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Applications

AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations

Adrià Pérez, Pablo Herrera-Nieto, Stefan Doerr, and Gianni De Fabritiis

J. Chem. Theory Comput.

2020

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Applications

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

Galvelis, Raimondas; Doerr, Stefan; Damas, João M; Harvey, Matt; De Fabritiis, Gianni

Journal of chemical information and modeling

2019

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Applications

From target to drug: generative modeling for the multimodal structure-based ligand design

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

Molecular pharmaceutics

2019

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Applications

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

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

Bioinformatics

2019

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Applications

DeltaDelta neural networks for lead optimization of small molecule potency

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

Chemical science

2019

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Applications

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

Scientific Reports

2019

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Applications

Shape-based generative modeling for de novo drug design

Skalic, Miha; Jiménez, José; Sabbadin, Davide; De Fabritiis, Gianni

Journal of chemical information and modeling

2019

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Applications

K deep: protein–ligand absolute binding affinity prediction via 3d-convolutional neural networks

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

Journal of chemical information and modeling

2018

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Applications

Molecular-simulation-driven fragment screening for the discovery of new CXCL12 inhibitors

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

Journal of chemical information and modeling

2018

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Fragment Based Drug Discovery

Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs

Ferruz, Noelia; Doerr, Stefan; Vanase-Frawley, Michelle A; Zou, Yaozhong; Chen, Xiaomin; Marr, Eric S; Nelson, Robin T; Kormos, Bethany L; Wager, Travis T; Hou, Xinjun; Villalobos, Anabella; Sciabola, Simone; De Fabritiis, Gianni

Scientific reports

2018

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Protein-Ligand Binding

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

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

Bioinformatics

2018

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Applications

PathwayMap: molecular pathway association with self-normalizing neural networks

Jimenez, Jose; Sabbadin, Davide; Cuzzolin, Alberto; Martinez-Rosell, Gerard; Gora, Jacob; Manchester, John; Duca, Jose; De Fabritiis, Gianni

Journal of chemical information and modeling

2018

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Applications

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

Nature chemistry

2017

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Conformational Studies

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

Doerr, Stefan; Giorgino, Toni; Martínez-Rosell, Gerard; Damas, Joao M; De Fabritiis, Gianni

Journal of Chemical Theory and Computation

2017

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ACEMD/HTMD/AceCloud

DeepSite: protein-binding site predictor using 3D-convolutional neural networks

Jiménez, José; Doerr, Stefan; Martínez-Rosell, Gerard; Rose, Alexander S; De Fabritiis, Gianni

Bioinformatics

2017

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Applications

Dimensionality reduction methods for molecular simulations

Doerr, Stefan; Ariz-Extreme, Igor; Harvey, Matthew J; De Fabritiis, Gianni

arXiv preprint arXiv:1710.10629

2017

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Theory

Optimizing Proteins and Ligands for Computerized Drug Discovery

Damas, João; Cuzzolin, Alberto; Galvelis, Raimondas; Doerr, Stefan; Martínez-Rosell, Gerard; Harvey, Matt; De Fabritiis, Gianni

2017

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Applications

PlayMolecule ProteinPrepare: a web application for protein preparation for molecular dynamics simulations

Martínez-Rosell, Gerard; Giorgino, Toni; De Fabritiis, Gianni

Journal of chemical information and modeling

2017

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Applications

Drug discovery and molecular dynamics: methods, applications and perspective beyond the second timescale

Martinez-Rosell, Gerard; Giorgino, Toni; Harvey, Matt J; de Fabritiis, Gianni

Current topics in medicinal chemistry

2017

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Applications

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

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

Scientific reports

2016

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Membrane Proteins

HTMD: high-throughput molecular dynamics for molecular discovery

Doerr, S; Harvey, MJ; Noé, Frank; De Fabritiis, G

Journal of chemical theory and computation

2016

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ACEMD/HTMD/AceCloud

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

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

Scientific reports

2016

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Protein-Ligand Binding

Binding kinetics in drug discovery

Ferruz, Noelia; De Fabritiis, Gianni

Molecular Informatics

2016

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Protein-Ligand Binding

HTMD: A complete software workspace for simulation-guided drug design

Doerr, Stefan; Harvey, Matt; De Fabritiis, Gianni

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY

2015

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ACEMD/HTMD/AceCloud

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

Martí-Solano, Maria; Iglesias, Alba; de Fabritiis, Gianni; Sanz, Ferran; Brea, José; Loza, M Isabel; Pastor, Manuel; Selent, Jana

Molecular pharmacology

2015

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Fragment Based Drug Discovery

AceCloud: molecular dynamics simulations in the cloud

Harvey, Matt J; De Fabritiis, Gianni

Journal of Chemical Information and Modeling

2015

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ACEMD/HTMD/AceCloud

Insights from fragment hit binding assays by molecular simulations

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

Journal of chemical information and modeling

2015

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Fragment Based Drug Discovery

Reranking docking poses using molecular simulations and approximate free energy methods

Lauro, G; Ferruz, Noelia; Fulle, Simone; Harvey, Matt J; Finn, Paul W; De Fabritiis, Gianni

Journal of chemical information and modeling

2014

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Theory

On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations

Doerr, S; De Fabritiis, G

Journal of chemical theory and computation

2014

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ACEMD/HTMD/AceCloud

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 F

Biochemical Journal

2014

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Applications

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

Bisignano, Paola; Doerr, Stefan; Harvey, Matt J; Favia, Angelo D; Cavalli, Andrea; De Fabritiis, Gianni

Journal of Chemical Information and Modeling

2014

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Conformational Studies

Kinetic modulation of a disordered protein domain by phosphorylation

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

Nature communications

2014

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Conformational Studies

Identification of slow molecular order parameters for Markov model construction

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

The Journal of chemical physics

2013

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ACEMD/HTMD/AceCloud

Visualizing the induced binding of SH2-phosphopeptide

Giorgino, T; Buch, I; De Fabritiis, G

Journal of chemical theory and computation

2012

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Protein-Ligand Binding

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 of the American Chemical Society

2012

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Conformational Studies

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

Harvey, Matthew J; De Fabritiis, Gianni

Drug discovery today

2012

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Theory

Kinetic characterization of the critical step in HIV-1 protease maturation

Sadiq, S Kashif; Noé, Frank; De Fabritiis, Gianni

Proceedings of the National Academy of Sciences

2012

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Conformational Studies

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

Buch, Ignasi; Giorgino, Toni; De Fabritiis, Gianni

Proceedings of the National Academy of Sciences

2011

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Protein-Ligand Binding

A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A

Giorgino, Toni; De Fabritiis, Gianni

Journal of Chemical Theory and Computation

2011

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Applications

Optimized potential of mean force calculations for standard binding free energies

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

Journal of Chemical Theory and Computation

2011

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Applications

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

Buch, I; Harvey, Matt J; Giorgino, T; Anderson, DP; De Fabritiis, G

Journal of chemical information and modeling

2010

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Applications

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

Selent, Jana; Sanz, Ferran; Pastor, Manuel; De Fabritiis, Gianni

PLoS Computational Biology

2010

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Membrane Proteins

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

Sadiq, S Kashif; De Fabritiis, Gianni

Proteins: Structure, Function, and Bioinformatics

2010

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Conformational Studies

An implementation of the smooth particle mesh Ewald method on GPU hardware

Harvey, MJ; De Fabritiis, G

Journal of Chemical Theory and Computation

2009

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Conformational Studies

ACEMD: Accelerating biomolecular dynamics in the microsecond time scale

Harvey, MJ; Giupponi, G; De Fabritiis, G

Journal of Chemical Theory and Computation

2009

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ACEMD/HTMD/AceCloud

The impact of accelerator processors for high-throughput molecular modeling and simulation

Giupponi, G; Harvey, MJ; De Fabritiis, G

Drug discovery today

2008

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Theory
International And EU Funded Projects
A cloud application platform for rational drug discovery using high throughput molecular dynamics.
European SME innovation Associate(H2020-INNOSUP-02-2016, Grant Agreement 739649)
Computer-Centric Fragment Based Ligand Discovery for the Development of candidate molecules targeting the chemkine system.
Nuclis d’Innovació Tecnològica 2014. Acció, Generalitat de Catalunya. Nuclis Transnacionals Programa Bilateral Catalunya-Israel, Project nr. RDIS14-1-0002. 2014-2016
Feasibility assessment of a cloud application platform for rational drug design using high-throughput.
H2020 SME Instrument 2014, Grant Agreement nr. 674659. 2015
A Centre of Excellence in Computational Biomedicine.
H2020-EINFRA-2015-1, Grant Agreement nr. 675451. 2016-2019
A Centre of Excellence in Computational Biomedicine.
H2020-INFRAEDI-02-2018, Grant Agreement nr. 823712. 2019-2023