Welcome to the Multiscale lab

Computational sciences 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.

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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. In this new research line we develop machine learning approaches applied to the biological data. We are particularly interested in dimensionality reduction, artificial neural networks, unsupervised learning, reinforcement learning, sparce coding, deep and hierarchical 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

People

Current member of our research group

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

Current group
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
  • PhD position - PhD in artificial neural networks in structural bioinformatics
  • 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
  • Staff scientist - Acellera is offering a position for scientific programmer/medicinal chemist
  • PhD position - PhD in protein-protein recognition and design
  • PhD position - PhD in intrinsically disordered proteins

Contact

PRBB

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

Email: gianni.defabritiis at upf.edu