Computational Biology and Simulation of Biological Systems

We focus on computational modeling and simulations of biological systems at molecular- and mesoscale. Structural characterization and functional mechanisms of these systems need to be elucidated, to understand diseases and develop treatments behind dysfunctions. In this framework, the main research lines are:

  • Protein folding and protein-protein interaction

  • Cell membrane penetration mechanisms of peptides

  • Computer simulations and machine learning applied in the pharmaceutical landscape

  • Signal transduction network modeling to investigate cell pathways

Key Projects

Drug Discovery for Chagas Disease


From medicinal plant to mechanism, target deconvolution of phytochemicals for Trypanosoma cruzi

VIRTUOUS


Virtual tongue to predIct the oRganoleptic profile of mediterranean IngredienTs and their effect on hUman hOmeostasis by means of an integrated compUtational multiphysicS platform

Cell-penetrating peptides


Elucidating the molecular mechanisms of translocation of Cell Penetrating Peptides

 

Selected Publications

  • M. Malavolta, L. Pallante, B. Mavkov, F. Stojceski, G. Grasso, A. Korfiati, S. Mavroudi, A. Kalogeras, C. Alexakos, V. Martos, D. Amoroso, G. Di Benedetto, D. Piga, K. Theofilatos & M. A. Deriu. A survey on computational taste predictors. Eur Food Res Technol. 03/2022. DOI: 10.1007/s00217-022-04044-5

  • E. Trofimenko, G. Grasso, M. Heulot, N. Chevalier, M. A Deriu, G. Dubuis, Y. Arribat, M. Serulla Llorens, S. Michel, G. Vantomme, F. Ory, J. Puyal, F. Amati, A. Lüthi, A. Danani, and C. Widmann, “Genetic, cellular and structural characterization of the membrane potential-dependent cell-penetrating peptide translocation pore”, eLife, DOI:10.7554/eLife.69832 (2021)

  • M. Serulla, G. Ichim, F. Stojceski, G. Grasso, S. Afonin, T. Schober, R. Roth, C. Godefroy, P.E. Milhiet, K. Das, A.G. Saez, A. Danani and C. Widmann, “TAT-RasGAP 317-326 kills cells by targeting inner leaflet-enriched phospholipids”, PNAS , DOI: 10.1073/pnas.2014108117 (2021)

  • G. Grasso , A. Di Gregorio , B. Mavkov, D. Piga, G. Falvo D’Urso Labate, A. Danani, and M.A. Deriu, “Fragmented blind docking: a novel protein-ligand binding prediction protocol “, Journal of Biomolecular Structure and Dynamics, 2021 Oct 12;1-10, DOI: 10.1080/07391102.2021.1988709.

  • L. Pallante, M. Malavolta, G. Grasso, A. Korfiati, S. Mavroudi, B. Mavkov, A. Kalogeras, C. Alexakos, V. Martos, D. Amoroso, G. di Benedetto, D. Piga, K. Theofilatos, M. A. Deriu. On the human taste perception: Molecular-level understanding empowered by computational methods, Trends in Food Science & Technology, 10/2021. DOI: 10.1016/j.tifs.2021.07.013

  • A. Rapallo, R. Gaspari , G. Grasso , A. Danani, “Extended Diffusion Theory: recovering dynamics from biased/accelerated molecular simulations”, Journal of Computational Chemistry, DOI: 10.1002/jcc.26474

  • S. Errico, G. Lucchesi, D. Odino, S. Muscat, C. Capitini, C. Bugelli, C. Canale, R. Ferrando, G. Grasso, D. Barbut, M. Calamai, A. Danani, M. Zasloff, A. Realini, G. Caminati, M. Vendruscolo, F. Chiti, “Making biological membrane resistant to the toxicity of misfolded protein oligomers: a lesson from trodusquemine”, Nanoscale, 2020, 12, 22596-22614, DOI: 10.1039/D0NR05285J

  • G. Grasso, A. Danani, “Molecular Simulations of Amyloid Beta Assemblies “, Advances in Physics: X, 5:1, 1770627, DOI:10.1080/23746149.2020.1770627

Contact

Prof. Andrea Danani

Professor at IDSIA

Personal website