Computational Science Laboratory
Computation applied to science
The group research interests are rooted in application of computation to solve real world problems with a view that computation and intelligence are very much the same thing. Specifically, we develop new methods, programs and algorithms that we apply to AI, 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, Biogen, Novartis, etc.
Highlights
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
D3R 2018 challenge. We won two sub-challenges in the D3R 2018 drug discovery blind challenge in collaboration with Acellera related to binding affinity and pose prediction of protein-ligand complexes.
LogP SAMPL 2018 challenge. We arrived second to the logP small molecule blind prediction challenge.
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.
Computational Science 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
- Gianni De Fabritiis - Head of Computational Science laboratory at University Pompeu Fabra, Icrea research professor, Founder at Acellera
- Irene Escolar Project Manager at University Pompeu Fabra
- Dominik Lemm - Phd student at University Pompeu Fabra
- Jose Jimenez - Phd student at University Pompeu Fabra
- Alejandro Varela - Phd student at University Pompeu Fabra
- Pablo Herrera Nieto - Phd student at University Pompeu Fabra
- Stefan Doerr - Research Engineer at Acellera
- Adria Perez - PhD student at University Pompeu Fabra
- Alberto Cuzzolin - Collaborator, staff scientist at Acellera
- Gerard Martinez - Collaborator, Staff at Acellera
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