Welcome to the Multiscale lab

Applied computational sciences in biomedicine and more

The group research interests are rooted in computational sciences, currently with an application focus on biomedicine. Specifically, we develop new computational methods and algorithms, we apply them to simulate and understand biological data and we design molecules with therapeutic applications in mind.

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. Using large distributed computational resources (GPUGRID.net) we search novel therapeutic molecules. We are particularly active in molecular dynamics simulations, binding prediction, binding kinetics, Markov state models, online sampling methods, and software development (ACEMD, HTMD). The approach is completely computational driven for hypothesis generation, then experimentally validated. We also 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 that we generate. We are particularly interested in dimensionality reduction methods, artificial neural networks, unsupervised learning. We also look at new computational intelligence approaches in general.

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.

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
  • PhD position - PhD in protein-protein recognition and design
  • Non-specific - 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.

  • Staff scientist - Acellera is offering a position for scientific programmer/medicinal chemist
  • 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