Research lines

My group research interests are at the interface between computation and biology, with an application focus on biomedicine. Specifically, we develop new computational physics methods and apply them to understand biological problems mainly at the level of protein folding and binding. This knowledge is then used to design molecules with therapeutic applications in mind.

  • Biomedicine.

We search new molecules to alter protein behavior with possible therapeutic implications, using new simulation-based methods for drug discovery. We develop in-silico fragment based drug discovery methods to explore the binding chemical space of a target and simulate drug-like binding events for the determination of kinetics, affinities and poses. New small molecules and peptides developped are then tested experimentally.

  • Computational physics.

We develop new codes for molecular dynamics simulations (ACEMD) running on special hardware to maximize the data throughput and extend the window of exploration of biological phenomena by simulations. We also work on distributed, volunteer computing where we perform most of our calculations with the help of people worldwide donating their computer time (GPUGRID). In order to analyze all the data generated, we actively develop new analysis techniques based on machine learning and Markov state models (HTMD) to determine equilibrium observables which can then be directly compared with experiments.

  • Protein folding and binding.

We computationally investigate biological systems to understand the mechanisms of biological processes at the atomistic level. The goal is to be able to create solid, quantitative hypothesis of how proteins behaves, how chemical modifications alter binding and folding, discover hidden order in intrinsically disordered proteins and understand molecular recognition pathways between molecules. We try to confront it with experimental collaborators and to exploit this understanding to find new therapeutic solutions.

Communications

Talks

  • EMBO Meeting on Advances in PPI Interaction Analysis & Modulation, Sept. 9-12 2014, Marseille, France.

  • Gordon conference in computational chemistry, 20 July 2014 Mount Snow Resort, West Dover, VT

  • State of Free Energy Calculations in Drug Design, 19 May 2014 , Boston, USA.

  • The aspect of time in drug design, 24 March 2014, Schloss Rauischholzhausen, Germany.

  • Drug Screening: from Phenotype to Molecular modeling, 27 Feb 2014, Lyon, France.

  • Structure-Based Drug Design conference, BIO-IT, 19-21 June 2013, Cambridge, Massachusetts, USA.

  • Conference of the Russian Biophysical society, 3-7 June 2013, Moscow, Russia.
  • Conference of the american chemical society, 8-11 April 2013 New Orleans,USA.
  • Biomolecular Simulation 2013, 25-27 March 2013, Nottingham, UK.

  • G. De Fabritiis, Fragment based drug discovery by simulation, CDDD, computationally driven drug discovery, 4-6 February (2013).

  • G. De Fabritiis, Fragment based drug discovery by simulation, Drug Design 2012, Oxford, UK 26-28 September (2012).

  • G. De Fabritiis, Molecular recognition by simulations, 2nd Aegean Conference on Molecular Recognition, 5-10 June 2012.

  • G. De Fabritiis, Fragment-based drug design using molecular dynamics, 2012 Workshop on Free Energy Methods in Drug Design,May 21-23, Cambridge, Massachusetts, USA.

  • T. Giorgino, I. Buch, G. De Fabritiis, Molecular recognition of SH2-phosphopeptide by molecular dynamics, XI Jornadas de Bioinformática, Barcelona, Spain, 23-25 Jan (2012).

  • I. Buch, T. Giorgino, G. De Fabritiis, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations,Combining Experimental and Computational Techniques to Study Protein Behavior, Lugano, Swiss, 26-29 Sept 2011.

  • I. Buch, T. Giorgino, G. De Fabritiis, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations, SEQT XVI, Valencia, 18-21 Sept (2011).

  • I. Buch, T. Giorgino, G. De Fabritiis, Complete reconstruction of a protein-ligand binding process by molecular dynamics simulations, Molecular kinetics, Berlin, 4-6 Sept (2011).

  • I. Buch, T. Giorgino, G. De Fabritiis, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations, Frontiers in Protein Research, Lisbon, 4-7 May (2011).

  • M. Harvey, I. Buch, T. Giorgino, G. De Fabritiis, High-throughput molecular dynamics simulations on GPUs using ACEMD, Exploiting New Computer Architectures in Molecular Dynamics Simulations, London UK March 23 2011.

  • I. Buch, T. Giorgino, Gianni De Fabritiis, Reconstructing an enzyme-inhibitor binding process by molecular dynamics simulations, Breakthroughs in Molecular Simulations, Albany 2011, The 17th Conversation, Albany, NY, USA, June 14-18 2011.

  • Gianni De Fabritiis, Towards high-throughput molecular simulations, Exascale Challenges in Computational Biology, 13-15 December, 2010 - Barcelona, Spain.

  • I. Buch, T. Giorgino, G. De Fabritiis, Energetics, kinetics and binding pathway reconstruction for enzyme-inhibitor complex from high-throughput molecular dynamics simulations, Prize-awarded presentation // UK Young Modellers Forum 2010, London (UK), 10th December 2010.

  • Gianni De Fabritiis, Workshop on parallel applications in HPC, Zaragoza, Spain, 30th November 2010,

  • Toni Giorgino, M. D'Abramo, F. Gervasio, G. De Fabritiis. Exploring the kinetics of drug binding to the hERG channel through large-scale simulations, VPH2010, Bruxelles, Belgium, 30th September-1st October, 2010.

  • I. Buch, T. Giorgino, G. De Fabritiis, Energetics, kinetics and binding pathway reconstruction for enzyme-inhibitor complex from high-throughput molecular dynamics simulations // IV Meeting on High Performance Computing in Molecular Simulations, Madrid (Spain), 30th September-1st October 2010.

  • Gianni De Fabritiis, High-throughput molecular dynamics simulations using ACEMD on GPUs, Bio-molecular Simulations Workshop on Future Computing Architectures, Oak Ridge National Laboratory, Oak Ridge, USA, 16-17th September 2010.

  • Gianni De Fabritiis, Impact of GPUs for molecular dynamics simulations: The case of ACEMD and GPUGRID.net, Programming and Tuning Massively Parallel Systems Summer School (PUMPS), July 5-9, 2010 Barcelona.slides

  • I. Buch, T. Giorgino, G. De Fabritiis,Reliable and accurate prediction of ligand binding by high-throughput molecular dynamics simulations, 1st Prize-awarded presentation // XVIII Jornades de Biologia Molecular, Barcelona (Spain), 29-30th June 2010.

  • J. Selent, F.Sanz, M. Pastor, G. De Fabritiis, Sodium ions toggle the rotamer switch in sodium-sensitive dopaminergic G-protein coupled receptors, 28th Camerino-Cyprus-Noordwijkerhout Symposium, Camerino, May 16-20, 2010

  • I. Buch, T. Giorgino, G. De Fabritiis,High-throughput all-atom molecular dynamics simulations using distributed computing (slides), 1st Prize-awarded presentation // 24th Molecular Modeling Workshop, Erlangen (Germany), 15-16th March 2010.

  • J. Selent, F.Sanz, M. Pastor, G. De Fabritiis,Accelerated molecular dynamics simulations in the microseconds time scale: An application to sodium-sensitive G protein-coupled receptors (slides) // Expanding the frontiers of molecular dynamics simulations in biology, Barcelona (Spain), 23-25th November 2009.

  • T. Giorgino, G. De Fabritiis, Submitting and managing distributed computations: the researcher's interface to a BOINC project (slides) // 5th BOINC Workshop, Barcelona (Spain), 22-23th October 2009.

Posters

  • I. Buch, M. Harvey, T. Giorgino, D. Anderson, G. De Fabritiis, A distributed computing system for high-throughput calculations of free energies of binding using molecular dynamics simulations (poster) // Expanding the frontiers of molecular dynamics simulations in biology, Barcelona (Spain), 23-25th November 2009.

  • I. Buch, M. Harvey, T. Giorgino, D. Anderson, G. De Fabritiis, A distributed computing system for high-throughput calculations of free energies of binding using molecular dynamics simulations (poster) // ISC 2010, Hamburg Germany 30th May-3th June 2010.

Courses

Funding acknowledgments

  • HPC-EUROPA2
  • Fundació La Marató de TV3
  • Sony Computer Entertainment Spain
  • Nvidia Corporation
  • Ramon y Cajal program
  • EU research program (Virtual Physiological human)
  • National research plan
  • EU Marie Curie program
Copyright 2008-2011. All rights reserved.