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Why GPUGRID?

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Goal

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Methods

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Project team / Sponsors

GIANNI DE FABRITIIS, PhD - Principal Investigator. TONI GIORGINO, PhD - Scientist. STEFAN DOERR - PhD student. ADRIÀ PÉREZ - PhD student. Sponsored by Universitat Pompeu Fabra - Barcelona, Spain.

Scientific results

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Scientific publications

  1. Doerr, Stefan, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino and Gianni De Fabritiis. TorchMD: A Deep Learning Framework for Molecular Simulations. Journal of Chemical Theory and Computation (2021). DOI: 10.1021/acs.jctc.0c01343.

  3. Bollati, Michela, Luisa Diomede, Toni Giorgino et al. A novel hotspot of gelsolin instability triggers an alternative mechanism of amyloid aggregation. Computational and Structural Biotechnology Journal (2021). DOI: 10.1016/j.csbj.2021.11.025.

  5. Herrera-Nieto, Pablo, Adrià Pérez and Gianni De Fabritiis. Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations. Scientific Reports (2020). DOI: 10.1038/s41598-020-69322-2.

  7. Herrera-Nieto, Pablo, Adrià Pérez and Gianni De Fabritiis. Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. Journal of Chemical Information and Modeling (2020). DOI: 10.1021/acs.jcim.0c00381.

  9. Cossu, Federica, Luca Sorrentino, Elisa Fagnani, Mattia Zaffaroni, Mario Milani, Toni Giorgino and Eloise Mastrangelo. Computational and Experimental Characterization of NF023, A Candidate Anticancer Compound Inhibiting cIAP2/TRAF2 Assembly. Journal of Chemical Information and Modeling (2020). DOI: 10.1021/acs.jcim.0c00518.

  11. Martinez-Rosell, Gerard, Silvia Lovera, Zara A. Sands and Gianni De Fabritiis. PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations. Journal of Chemical Information and Modeling (2020). DOI: 10.1021/acs.jcim.9b01209.

  13. Rodríguez-Espigares, Ismael, Mariona Torrens-Fontanals, Johanna K. S. Tiemann et al. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature Methods (2020). DOI: 10.1038/s41592-020-0884-y.

  15. Wang, Jiang, Simon Olsson, Christoph Wehmeyer, Adrià Pérez, Nicholas E. Charron, Gianni de Fabritiis, Frank Noé and Cecilia Clementi. Machine Learning of Coarse-Grained Molecular Dynamics Force Fields. ACS Central Science (2019). DOI: 10.1021/acscentsci.8b00913.

  17. Martinez-Rosell, Gerard, Matt J. Harvey and Gianni De Fabritiis. Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors. Journal of Chemical Information and Modeling (2018). DOI: 10.1021/acs.jcim.7b00625.

  19. Ferruz, Noelia, Stefan Doerr, Michelle A. Vanase-Frawley et al. Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. Scientific Reports (2018). DOI: 10.1038/s41598-018-19345-7.

  21. Pérez, Adrià, Gerard Martínez-Rosell and Gianni De Fabritiis. Simulations meet machine learning in structural biology. Current Opinion in Structural Biology (2018). DOI: 10.1016/j.sbi.2018.02.004.

  23. Kapoor, Abhijeet, Gerard Martinez-Rosell, Davide Provasi, Gianni de Fabritiis and Marta Filizola. Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity. Scientific Reports (2017). DOI: 10.1038/s41598-017-11483-8.

  25. Plattner, Nuria, Stefan Doerr, Gianni De Fabritiis and Frank Noé. Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nature Chemistry (2017). DOI: 10.1038/nchem.2785.

  27. Doerr, Stefan, Toni Giorgino, Gerard Martínez-Rosell, João M. Damas and Gianni De Fabritiis. High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD. Journal of Chemical Theory and Computation (2017). DOI: 10.1021/acs.jctc.7b00480.

  29. Doerr, Stefan, Igor Ariz-Extreme, Matthew J. Harvey and Gianni De Fabritiis. Dimensionality reduction methods for molecular simulations. (2017). DOI: 10.48550/ARXIV.1710.10629.

  31. Martínez-Rosell, Gerard, Toni Giorgino, Matt J. Harvey and Gianni de Fabritiis. Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale. Current Topics in Medicinal Chemistry (2017). DOI: 10.2174/1568026617666170414142549.

  33. Ferruz, Noelia, Gary Tresadern, Antonio Pineda-Lucena and Gianni De Fabritiis. Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme. Scientific Reports (2016). DOI: 10.1038/srep30275.

  35. Doerr, S., M. J. Harvey, Frank Noé and G. De Fabritiis. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. Journal of Chemical Theory and Computation (2016). DOI: 10.1021/acs.jctc.6b00049.

  37. Stanley, Nathaniel, Leonardo Pardo and Gianni De Fabritiis. The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor. Scientific Reports (2016). DOI: 10.1038/srep22639.

  39. Stanley, Nathaniel, Santiago Esteban-Martín and Gianni De Fabritiis. Progress in studying intrinsically disordered proteins with atomistic simulations. Progress in Biophysics and Molecular Biology (2015). DOI: 10.1016/j.pbiomolbio.2015.03.003.

  41. Ferruz, Noelia, Matthew J. Harvey, Jordi Mestres and Gianni De Fabritiis. Insights from Fragment Hit Binding Assays by Molecular Simulations. Journal of Chemical Information and Modeling (2015). DOI: 10.1021/acs.jcim.5b00453.

  43. Doerr, S. and G. De Fabritiis. On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations. Journal of Chemical Theory and Computation (2014). DOI: 10.1021/ct400919u.

  45. Dainese, Enrico, Gianni De Fabritiis, Annalaura Sabatucci et al. Membrane lipids are key modulators of the endocannabinoid-hydrolase FAAH. Biochemical Journal (2014). DOI: 10.1042/BJ20130960.

  47. Stanley, Nathaniel, Santiago Esteban-Martín and Gianni De Fabritiis. Kinetic modulation of a disordered protein domain by phosphorylation. Nature Communications (2014). DOI: 10.1038/ncomms6272.

  49. Huang, Xuhui and Gianni De Fabritiis. Understanding Molecular Recognition by Kinetic Network Models Constructed from Molecular Dynamics Simulations. An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation (2014).

  51. Bisignano, P., S. Doerr, M. J. Harvey, A. D. Favia, A. Cavalli and G. De Fabritiis. Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations. Journal of Chemical Information and Modeling (2014). DOI: 10.1021/ci4006063.

  53. Lauro, G., N. Ferruz, S. Fulle, M. J. Harvey, P. W. Finn and G. De Fabritiis. Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods. Journal of Chemical Information and Modeling (2014). DOI: 10.1021/ci500309a.

  55. Venken, Tom, Arnout Voet, Marc De Maeyer, Gianni De Fabritiis and S. Kashif Sadiq. Rapid Conformational Fluctuations of Disordered HIV-1 Fusion Peptide in Solution. Journal of Chemical Theory and Computation (2013). DOI: 10.1021/ct300856r.

  57. Pérez-Hernández, Guillermo, Fabian Paul, Toni Giorgino, Gianni De Fabritiis and Frank Noé. Identification of slow molecular order parameters for Markov model construction. The Journal of Chemical Physics (2013). DOI: 10.1063/1.4811489.

  59. Harvey, Matthew J. and Gianni De Fabritiis. High-throughput molecular dynamics: the powerful new tool for drug discovery. Drug Discovery Today (2012). DOI: 10.1016/j.drudis.2012.03.017.

  61. Giorgino, T., I. Buch and G. De Fabritiis. Visualizing the Induced Binding of SH2-Phosphopeptide. Journal of Chemical Theory and Computation (2012). DOI: 10.1021/ct300003f.

  63. Bruno, Agostino, Gabriele Costantino, Gianni de Fabritiis, Manuel Pastor and Jana Selent. Membrane-Sensitive Conformational States of Helix 8 in the Metabotropic Glu2 Receptor, a Class C GPCR. PLoS ONE (2012). DOI: 10.1371/journal.pone.0042023.

  65. Harvey, M. J. and Gianni De Fabritiis. A survey of computational molecular science using graphics processing units: Survey of computational molecular science on GPUs. Wiley Interdisciplinary Reviews: Computational Molecular Science (2012). DOI: 10.1002/wcms.1101.

  67. Wright, David W., S. Kashif Sadiq, Gianni De Fabritiis and Peter V. Coveney. Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase. Journal of the American Chemical Society (2012). DOI: 10.1021/ja301565k.

  69. Sadiq, S. Kashif, Frank Noé and Gianni De Fabritiis. Kinetic characterization of the critical step in HIV-1 protease maturation. Proceedings of the National Academy of Sciences (2012). DOI: 10.1073/pnas.1210983109.

  71. Buch, Ignasi, S. Kashif Sadiq and Gianni De Fabritiis. Optimized Potential of Mean Force Calculations for Standard Binding Free Energies. Journal of Chemical Theory and Computation (2011). DOI: 10.1021/ct2000638.

  73. Buch, Ignasi, Toni Giorgino and Gianni De Fabritiis. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proceedings of the National Academy of Sciences (2011). DOI: 10.1073/pnas.1103547108.

  75. Giorgino, Toni and Gianni De Fabritiis. A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A. Journal of Chemical Theory and Computation (2011). DOI: 10.1021/ct100707s.

  77. Giorgino, Toni, M.J. Harvey and Gianni de Fabritiis. Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations. Computer Physics Communications (2010). DOI: 10.1016/j.cpc.2010.04.007.

  79. Buch, I., M. J. Harvey, T. Giorgino, D. P. Anderson and G. De Fabritiis. High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing. Journal of Chemical Information and Modeling (2010). DOI: 10.1021/ci900455r.

  81. De Lomana, Adrián López García, Qasim K. Beg, G. De Fabritiis and Jordi Villà-Freixa. Statistical Analysis of Global Connectivity and Activity Distributions in Cellular Networks. Journal of Computational Biology (2010). DOI: 10.1089/cmb.2008.0240.

  83. Selent, Jana, Ferran Sanz, Manuel Pastor and Gianni De Fabritiis. Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors. PLoS Computational Biology (2010). DOI: 10.1371/journal.pcbi.1000884.

  85. Sadiq, S. Kashif and Gianni De Fabritiis. Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing. Proteins: Structure, Function, and Bioinformatics (2010). DOI: 10.1002/prot.22806.

  87. Harvey, M. J. and G. De Fabritiis. An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. Journal of Chemical 
  88. Theory and Computation (2009). DOI: 10.1021/ct900275y.

  90. Guix, Francesc X., Gerard Ill-Raga, Ramona Bravo et al. Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation. Brain (2009). DOI: 10.1093/brain/awp023.

  92. Harvey, M. J., G. Giupponi and G. De Fabritiis. ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. Journal of Chemical Theory and Computation (2009). DOI: 10.1021/ct9000685.

  94. Harvey, M. J., G. De Fabritiis and G. Giupponi. Accuracy of the lattice-Boltzmann method using the Cell processor. Physical Review E (2008). DOI: 10.1103/PhysRevE.78.056702.
  95. De Fabritiis, G., P. V. Coveney and J. Villà-Freixa. Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics. Proteins: Structure, Function, and Bioinformatics (2008). DOI: 10.1002/prot.22036.

  97. Giupponi, G., M.J. Harvey and G. De Fabritiis. The impact of accelerator processors for high-throughput molecular modeling and simulation. Drug Discovery Today (2008). DOI: 10.1016/j.drudis.2008.08.001.

  99. Fabritiis, Gianni De, Sebastien Geroult, Peter V. Coveney and Gabriel Waksman. Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain. Proteins: Structure, Function, and Bioinformatics (2008). DOI: 10.1002/prot.22027.

  101. Delgado-Buscalioni, R, P V Coveney and G De Fabritiis. Towards multi-scale modelling of complex liquids using hybrid particle—continuum schemes. Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science (2008). DOI: 10.1243/09544062JMES746.

  103. Lloyd, Sharon, Dave Gavaghan, Andrew Simpson et al. Integrative Biology — the challenges of developing a collaborative research environment for heart and cancer modelling. Future Generation Computer Systems (2007). DOI: 10.1016/j.future.2006.07.002.

  105. De Fabritiis, G. Performance of the Cell processor for biomolecular simulations. Computer Physics Communications (2007). DOI: 10.1016/j.cpc.2007.02.107.

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