Welcome to the Computational Science Laboratory

Computational science in biomedicine and machine learning

The group research interests are rooted in application of computation to solve real world problems. Specifically, we develop new methods and algorithms and we apply them to computational chemistry, drug design, protein folding, etc.

The group and the spin-off company Acellera has collaborated with major industries worldwide like Sony, Nvidia, HTC mobile, UCB, Pfizer, etc.

PlayMolecule

PlayMolecule is a platform for drug discovery and structural biology applications based on physics-based simulations and deep learning. Try it at:

http://www.playmolecule.org

High-throughput molecular dynamics In 2015 we relased the HTMD Python environment for simulation-based molecular discovery.
Molecular dynamics engine on GPUs Since 2006 ACEMD has pioneered the use of acellerator processors for general purpose molecular simulations.
Distributed computing GPUGRID.net is currently one of the two largest distributing computing project worldwide.
Industrial Spin-Offs Acellera Ltd is a spin-off created in 2006 to accelerate the transition to simulation-based discovery in drug discovery.
Community access Everybody can access most of our tools and predictors via playmolecule.org
Scientific Publications We have published over 80 research articles.

Research

Research Lines

Biomedicine. We use large distributed computational resources (GPUGRID.net) with thousands of GPUs for molecular dynamics simulations, binding prediction, binding kinetics, Markov state models, online sampling methods (ACEMD, HTMD). The approach is computational driven but we like to collaborate with experimental laboratories and industries where we work by rationalizing experimental results.

Machine Intelligence. We develop machine learning approaches applied to physics, chemistry and biology. We are particularly interested in reinforcement learning, Bayesian networks and deep learning.

Software

HTMD - HTMD is a Python platform for computational biology, including molecular simulations, docking, Markov state models, molecule manipulation, build tools for Amber and Charmm, visualization (webGL and VMD), adaptive sampling and more. Imagine setting up an entire computational experiment in a single, simple Python script.

ACEMD - ACEMD has pioneered the use of GPUs for molecular simulations allowing for high-throughput simulations and ultimately leading to HTMD. ACEMD is still one of top molecular dynamics code, simple to use with a NAMD like syntax and compatible with input files from Charmm and Amber.

Web resources

Playmolecule - Most of our methods, predictors and machine learning approaches are publicly available via this webGL enabled site.

Multiscale Laboratory GitHub - More tools are available in our github account. Follow us there.

HTMD github repository - HTMD main repository publicly accessible in github. Contribute!

The youtube channel of Acellera - Acellera posts a lot of material here

People

Current members of our research group

In our group we always value having the best people from different background and expertises

Current group

Apply

Apply for a position

We are always looking for talented people who would like to join our laboratory. We praise on diversity of expertises, e.g. mathematics, chemistry, computer science, statistics, physics, biology, biotechnology, etc. If you are a passionate, hard working, self-motivated person with the ambition to do great science, send us an email at gianni.defabritiis@upf.edu.

OPEN POSITIONS

  • Postdoctoral position - Develop machine learning models in physics and chemistry applied to drug discovery
  • PhD position - PhD in deep learning in computational structural biology
  • General- If you are interested in doing a specific project idea with us send a CV and motivation letter to gianni.defabritiis@upf.edu

CLOSED POSITIONS

These positions are closed but we might have similar ones in the future.

  • PhD position - PhD in artificial neural networks in structural bioinformatics
  • PhD position - PhD in protein-protein recognition and design
  • PhD position - PhD in intrinsically disordered proteins

Contact

Gianni De Fabritiis, GRIB, Barcelona Biomedical Research Park (PRBB),
C/ Dr. Aiguader 88, 08003, Barcelona, Spain.

Email: gianni.defabritiis at upf.edu

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