Research groups

Computational Biophysics group of GRIB

The Computational Biophysics group studies protein dynamics, kinetics and energetics using mainly molecular dynamics simulations on graphics processing units (GPUs) and GPUGRID. The group attempts to solve new scientific problems by developing new methodologies, software and ideas for bridging between the atomistic scale and the biological molecular scale. The software developed by the group is commerzialised by the SME Acellera

The current research lines of the group are:

  • 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.

The Computational Biophysics group of GRIB, led by Gianni de Fabritiis, is integrated in the Research Programme on Biomedical Informatics, GRIB. The GRIB is a joint research programme of the Hospital del Mar Medical Research Institute (IMIM) and the Department of Experimental and Health Sciences of the Universitat Pompeu Fabra. The GRIB mission is to develop and apply computational methods and information technologies for a better understanding and prediction of biological phenomena, giving especial emphasis to those related to the human diseases, their prevention, diagnosis and pharmacological treatment.

Main projects

  • 1.

    CompBioMed: A Centre of Excellence in Computational Biomedicine

    CompBioMed is a user-driven Centre of Excellence in Computational Biomedicine, to nurture and promote the uptake and exploitation of high performance computing within the biomedical modelling community. European project funded by the H2020 for period 2016-2019.

    http://www.compbiomed.eu/

  • 2.

    Conformational kinetics, binding and modulation of disordered protein domains

    2015-2017 (BIO2014-53095-P) MINECO

Website

Institutions

Bioinformatics expertise:

Group Leader:

Gianni de Fabritiis

PI

Contact:

Chus Donlo

Bioinformatics services offered

  • HTMD

    High-throughput molecular dynamics is our concept for molecular simulation based discovery. The software implementation in Python is currently available for download.

    http://www.htmd.org

  • 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.

    https://www.acellera.com/products/molecular-dynamics-software-GPU-acemd/