Science

Innovation in the drug discovery pipeline

Science

Acellera is actively involved in research and development. Since 2006 we support applied research for the development of biomedical simulation methods via agreements with academic institutions.

Furthermore, Acellera creates new software and hardware infrastructure for performing biomolecular simulations in high-throughput. Salient examples are Metrocubo, the Acellera GPU chassis, and the AceCloud interface. The latter two examples are currently patent pending

We would be happy to consider scientific collaborations with interested parties to demonstrate the potentiality of biomolecular simulations. We are open to research projects (e.g. European projects) as well as other collaboration formats.

Acellera research

Click on the categories to see Acellera’s research on that topic.

Applications

Conformational studies

Protein-Ligand Binding

Membrane Proteins

Theory

ACEMD

HTMD

ACECLOUD

Fragment Based

Selected Publications

Applications

Miha Skalic, Gerard Martínez-Rosell, José Jiménez, Gianni De Fabritiis; PlayMolecule BindScope: Large scale CNN-based virtual screening on the web, Bioinformatics, (2018) , bty758, https://doi.org/10.1093/bioinformatics/bty758
Miha Skalic, Alejandro Varela-Rial, José Jiménez, Gerard Martínez-Rosell, Gianni De Fabritiis; LigVoxel: Inpainting binding pockets using 3D-convolutional neural networks, Bioinformatics (2018) https://doi.org/10.1093/bioinformatics/bty583
José Jiménez Luna, Miha Skalic, Gerard Martinez-Rosell, and Gianni De Fabritiis. KDEEP: Protein-ligand absolute binding affinity prediction via 3D-convolutional neural networks. Journal of Chemical Information and Modeling. (2018) DOI: 10.1021/acs.jcim.7b00650
G. Martinez-Rosell, T. Giorgino, G. de Fabritiis PlayMolecule ProteinPrepare: a web application for protein preparation for molecular dynamics simulations in J. Chem. Inf. Model 2017, June 10.
N Plattner, S Doerr, G de Fabritiis, F Noé Complete protein-protein association kinetics in atomic details revealed by molecular dynamics simulations and Markov modelling in Nature Chemistry 2017 June 5.
G Martinez-Rosell, T Giorgino, MJ Harvey, G de Fabritiis, Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale in Curr Top Med Chem. 2017 Apr 14.
E. Dainese, G. De Fabritiis, A. Sabatucci, S. Oddi, CB. Angelucci, C. Di Pancrazio, I. Giorgino, N. Stanley, M Del Carlo, B.F. Cravatt, M. Maccarrone. Membrane lipids are key modulators of the endocannabinoid-hydrolase FAAH. Biochem J. 2014 Feb 1;457(3):463-72.
T. Giorgino and G. De Fabritiis, A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A, J. Chem. Theory Comput., 7 , 1943–1950 (2011). pdf
I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson and G. De Fabritiis. High-throughput all-atom molecular dynamics simulations using distributed computing. J. Chem. Inf. and Mod. 50, 397 (2010).

Ongoing international and EU funded projects

CompBioMed

A Centre of Excellence in Computational Biomedicine. H2020-EINFRA-2015-1, Grant Agreement nr. 675451. 2016-2019

HTMD

Feasibility assessment of a cloud application platform for rational drug design using high-throughput. H2020 SME Instrument 2014, Grant Agreement nr. 674659. 2015

CCFBLD-CHEMO

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

Science

Innovation in the drug discovery pipeline

Science

Acellera research

Applications

Conformational studies

Protein-Ligand Binding

Membrane Proteins

Theory

ACEMD

HTMD

ACECLOUD

Fragment Based

Selected Publications

Applications

Conformational studies

Protein-Ligand Binding

Fragment Based Drug Discovery

Membrane proteins

Theory

ACEMD references

HTMD references

AceCloud references

Ongoing international and EU funded projects

CompBioMed

HTMD

CCFBLD-CHEMO

R&D	Headquarters
PRBB	Devonshire House
Dr Aiguader, 88	582 Honeypot Lane
08003 Barcelona, Spain	Stanmore, Middlesex, England (HA7 1JS)