Federico Ballabio
Email:
federico.ballabio@unimi.it
Cicle:
XXXVII A.Y.
2021 - 2022
Supervisor:
Carlo Camilloni
Title:
Integrative modelling of molecular recognition processes by molecular dynamics simulations … read more
External links: GoogleScholar
ORCID
PhD Seminars:
| Date |
Title |
Speakers |
| 15/10/2021 |
Apomixis (clonal seeds): breeding technology of the 2020s |
Dr. Peter van Dijk |
| 21/10/2021 |
FROM PLASTICS TO LIQUID-POLYMERS: A NEW ENVIRONMENTAL TREATH |
Dr. Stefano Magni |
| 29/10/2021 |
How studying intercellular communication pathways in plant meristems can generate opportunities for crop improvement |
Dr. Rüdiger Simon |
| 03/11/2021 |
USE OF AN OLD DRUG FOR NEW DISEASES- REPOSITIONING OF THALIDOMIDE FOR COVID-19 AND KAWASAKI DISEASE |
Dr. Luisa Guerrini |
| 24/11/2021 |
FROM STRUCTURAL STUDIES OF ION CHANNELS TO THE DEVELOPMENT OF SYNTHETIC PEPTIDES FOR PHARMACEUTICAL AND BIOTECHNOLOGICAL APPROACHES |
Dr. Andrea Saponaro |
| 26/11/2021 |
Environmental control of shoot meristem shape during floral transition |
Dr. George Coupland |
| 15/12/2021 |
DISSECTING THE ROLE OF THE TWO-PORE POTASSIUM CHANNELS (K2P) IN THE HUMAN GLIOBLASTOMA PROGRESSION |
Dr. Federico Brandalise |
| 02/02/2022 |
TRANSCRIPTION AND DYNAMICS OF TRANSPOSABLE ELEMENTS KEEPS ON FIRE THE GENOME OF HUMAN T LYMPHOCYTES |
Dr. Beatrice Bodega |
| 11/03/2022 |
Cytoskeletal tension sets nuclear size |
Dr. Paolo Maiuri |
| 18/03/2022 |
How a digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule |
Dr. Kay Schneitz |
| 21/03/2022 |
Using graph theory to understand the conceptual basis of biological systems |
Dr. Jeremy Gunawardena |
| 23/03/2022 |
EPIGENETIC INTEGRATION OF HORMONAL AND ENVIRONMENTAL SIGNALS IN PLANTS |
Dr. Giorgio Perrella |
| 24/03/2022 |
DNA liquid crystals: back to the origin of life |
Dr. Giuliano Zanchetta |
| 01/04/2022 |
3.8 billion years of mechanotransduction: From osmoregulation to the sense of touch |
Dr. Boris Martinac |
| 08/04/2022 |
From single cells to flowers: Gene-regulatory mechanisms controlling organ specification in Arabidopsis flowers |
Dr. Kerstin Kaufmann |
| 29/04/2022 |
Role of plant hormones in the regulation of plant development and adaptation to environmental conditions |
Dr. Eva Benkova |
| 04/05/2022 |
CELL REPLACEMENT THERAPY FOR HUNTINGTON DISEASE |
Dr. Dario Besusso |
| 10/05/2022 |
Modeling the molecular states of brain cells |
Dr. Jose Davila-Velderrain |
| 28/06/2022 |
"Eppur si muove" - Dynamics and recognition in biomolecules |
Dr. Luca Mollica |
| 07/07/2022 |
Investigation of G-protein specificity and bias agonism at the beta-2 adrenergic receptor |
Dr. Marina Casiraghi |
| 12/07/2022 |
Machine learning for in-silico drug discovery and precision medicine |
Dr. Sergio Decherchi |
| 28/10/2022 |
Accurate modeling DNA deformability and its role in protein binding |
Prof. Martin Zacharias |
| 04/11/2022 |
Harnessing the Power of Computer Graphics for Structural Biology with Blender & Molecular Nodes |
Dr. Brady Johnston |
| 11/11/2022 |
Coordination of bacterial cell envelope biogenesis |
Prof. Waldemar Vollmer |
| 25/11/2022 |
Study of the effects of using different water-saving strategies on plant growth, yield and photosynthesis in different crops grown under Mediterranean climate conditions in northeastern Morocco |
Prof. Kamal Aberkani |
| 27/01/2023 |
Twisting the boundaries: Role of DNA topoisomerases at the nuclear lamina |
Dr. Stefano Manzo |
| 31/01/2023 |
MITOCHONDRIA NETWORK AS A CENTRAL HUB IN THE CONTROL OF PROTEOSTASIS AND AGEING |
Prof. Marco Sandri |
| 09/02/2023 |
How HIV uses its capsid to promote infection and evade innate immunity |
Dr. Guido Papa |
| 21/03/2023 |
Neuronal differentiation and neurodegeneration: the dual role of sphingolipids |
Emma Carsana |
| 21/04/2023 |
Computational modeling: a quantitative tool to investigate cardiac cellular electrophysiology |
Prof. Stefano Severi |
| 04/05/2023 |
Prediction of phase separation of IDRs and coiled-coil domains |
Dr. Loren Hough |
| 04/05/2023 |
The structural architecture of an α-synuclein toxic oligomer |
Prof. Salvador Ventura |
| 15/05/2023 |
Understanding biomolecular behaviour with mass photometry |
Dr. Perla Vega Dominguez |
| 23/06/2023 |
The cold side of connectivity. A journey in the Southern Ocean with Antarctic fish |
Prof. Chiara Papetti |
| 04/07/2023 |
Molecular and functional heterogeneity in dorsal and ventral oligodendrocyte progenitor cells of the mouse forebrain in response to DNA damage |
Prof. Enrica Boda |
| 14/07/2023 |
Bacterial exoskeletons and where to find them: the Bacillus anthracis case |
Dott.ssa Antonella Fioravanti |
| 18/07/2023 |
Uno sguardo ad ampio spettro sul futuro della citometria a flusso |
Dr. Enrico Ghersi |
| 20/10/2023 |
Chaperone regulation of the protein condensation and aggregation continuum in Alzheimer's disease |
Prof. Claudio Gomes |
| 03/11/2023 |
Conformational ensembles of the human intrinsically disordered proteome |
Prof. Kresten Lindorff-Larsen |
| 10/11/2023 |
Markov-state modeling of biomolecular systems |
Dr. Toni Giorgino |
| 24/11/2023 |
Molecular evolution and host adaptation of human-infecting dsDNA viruses |
Dr. Manuela Sironi |
| 02/02/2024 |
What the structures of amyloids teach us about amyloid pathology |
Prof. Joost Schymkowitz |
| 10/04/2024 |
New Unexpected Photoreceptors with potential Optogenetic Applications |
Prof. Peter Hegemann |
| 10/09/2024 |
Molecular Simulations for Molecular Design |
Prof. Giorgio Colombo |
PhD Courses:
| Starting Date |
Ending Date |
Title |
Place |
| 18/01/2022 |
01/02/2022 |
Foundations of Academic Writing |
Online |
| 14/02/2022 |
18/02/2022 |
MOLECULAR AND CELLULAR BIOLOGY: METHODS AND COMMUNICATION OF RESULTS |
Department of Biosciences - UniMi |
| 08/03/2022 |
09/03/2022 |
INTEGRATED STRUCTURAL BIOLOGY |
Department of Biosciences - UniMi / IFOM-IEO |
| 21/03/2022 |
24/03/2022 |
Language Coaching - Interpersonal Skills: Presentation Skills |
Online |
| 22/03/2022 |
23/03/2022 |
Basic Introductory Course on IP and Patents |
Online |
| 01/04/2022 |
29/04/2022 |
Open Science |
Online |
| 06/05/2022 |
06/05/2022 |
Data Management |
Online |
| 11/05/2022 |
01/07/2022 |
COMPUTATIONAL STATISTICS WITH R AND PYTHON |
Department of Public Health Sciences - UniMi |
| 06/06/2022 |
09/06/2022 |
INTRODUCTION TO SCIENTIFIC PROGRAMMING WITH PYTHON |
Department of Earth Sciences - UniMi |
| 28/06/2022 |
06/07/2022 |
New Media Communication |
Online |
| 11/07/2022 |
12/07/2022 |
Research Assessment |
Online |
| 11/09/2022 |
13/09/2022 |
BASIC STATISTICS FOR BIOLOGICAL DATA |
Department of Pharmaceutical Sciences - UniMi |
| 21/09/2022 |
21/09/2022 |
Introduction to Research Enhancement |
Online |
| 14/01/2023 |
14/01/2023 |
Research Integrity - Natural and physical sciences |
Online |
| 21/02/2023 |
21/02/2023 |
Research Integrity II |
Online |
| 10/03/2023 |
14/03/2023 |
Academic Writing: Research paper |
Online |
| 17/04/2023 |
18/04/2023 |
SUPPORTING TOOLS FOR DRUG-TARGET PRIORITISATION AND ANALYSIS OF BIOLOGICAL NETWORKS |
Laboratorio Interdisciplinare di Tecnologie Avanzate - UniMi |
| 22/05/2023 |
23/05/2023 |
Language coaching - Interpersonal Skills: Interview Skills |
Online |
| 13/06/2023 |
13/06/2023 |
Grantmanship I |
Online |
| 20/06/2023 |
28/06/2023 |
HPC@UNIMI: INDACO FOR DRUG DISCOVERY AND DEVELOPMENT |
Department of Pharmaceutical Sciences - UniMi |
| 30/06/2023 |
30/06/2023 |
Self Branding - PhD’s Skills and Employability |
Online |
| 26/09/2023 |
26/09/2023 |
Grantmanship II |
Online |
| 22/11/2023 |
19/01/2024 |
PROTEIN STRUCTURE PREDICTION AND DESIGN: HOW TO USE ALPHAFOLD AND OTHER AI METHODS FOR RESEARCH |
Department of Biosciences - UniMi |
| 19/02/2024 |
19/02/2024 |
Workshop on how to prepare a dissemination/communication plan |
UniMi |
| 19/02/2024 |
23/02/2024 |
Finding a job after the PhD |
UniMi |
| 19/02/2024 |
23/02/2024 |
Exploitation by means of business creation: spin-off and entrepreneurship from an academic point of view |
UniMi |
| 19/02/2024 |
23/02/2024 |
La valutazione della Sostenibilità Integrata per la Global Health |
UniMi |
| 19/02/2024 |
23/02/2024 |
Teaching and learning 1 |
UniMi |
| 19/02/2024 |
23/02/2024 |
Teaching and learning 2 |
UniMi |
| 19/02/2024 |
23/02/2024 |
The Art of Grantmanship |
UniMi |
Conferences / Workshops:
| Starting Date |
Ending Date |
Title |
Place |
| 18/02/2019 |
20/02/2019 |
CINECA: High Performance Molecular Dynamics |
CINECA - Casalecchio di Reno |
| 26/06/2019 |
26/06/2019 |
Interdisciplinary Aspects of Biomolecular Modelling |
Department of Biosciences - UniMi |
| 30/09/2019 |
03/10/2019 |
CINECA: Introduction to Parallel Computing with MPI and OpenMP |
CINECA - Segrate |
| 11/11/2019 |
13/11/2019 |
CINECA: Introduction to Fortran for Scientific Computing |
CINECA - Segrate |
| 05/02/2020 |
07/02/2020 |
CINECA: Introduction to Python programming |
CINECA - Segrate |
| 10/06/2020 |
15/07/2020 |
Schrödinger: Introduction to Molecular Modeling in Drug Discovery |
Online |
| 12/11/2020 |
13/11/2020 |
CINECA: Containerization in High Performance Computing |
Online |
| 09/12/2020 |
11/12/2020 |
CINECA: High Performance Bioinformatics |
Online |
| 14/11/2021 |
14/12/2021 |
Schrödinger: Introduction to Computational Antibody Engineering |
Online |
| 22/11/2021 |
26/11/2021 |
CINECA: Data Science and Deep Learning with Python |
Online |
| 20/06/2022 |
24/06/2022 |
EMBO: Small angle neutron and x-ray scattering from biomacromolecules in solution |
European Photon and Neutron Science Campus - Grenoble (France) |
| 05/09/2022 |
08/09/2022 |
Physics of Biomolecules: Structure, Dynamics and Function (7th Workshop) |
Bressanone |
| 06/02/2023 |
08/02/2023 |
CINECA: Python for Scientific Computing |
Online |
| 22/02/2023 |
22/02/2023 |
4EU+ Training Session: Introduction to Open Science and Research Integrity |
Online |
| 23/03/2023 |
23/03/2023 |
One-day workshop on last advancements in protein aggregation from both computational and experimental point of view |
Department of Biosciences - UniMi |
| 24/03/2023 |
24/03/2023 |
4EU+ Training session: Open Access and Open licences |
Online |
| 27/03/2023 |
29/03/2023 |
CINECA: Introduction to Scientific and Technical Computing in C |
Online |
| 03/05/2023 |
05/05/2023 |
CINECA: Introduction to Scientific and Technical Computing in C++ |
Online |
| 27/08/2023 |
31/08/2023 |
European Conference on Computational and Theoretical Chemistry (EuChemS CompChem 2023) |
Olympic Museum - Thessaloniki (Greece) |
| 20/11/2023 |
24/11/2023 |
CINECA: Advanced School on HPC Computing with GPU Accelerators |
Online |
| 06/12/2023 |
09/12/2023 |
EMBO: Computational structural biology |
EMBL Advanced Training Centre - Heidelberg (Germany) |
| 05/02/2024 |
08/02/2024 |
Physics of Biomolecules: Structure, Dynamics and Function (8th Workshop) |
Bressanone |
| 14/03/2024 |
16/03/2024 |
PhD retreat - XXXVII cycle |
Venezia |
| 24/04/2024 |
26/04/2024 |
NIC Days: Biomolecular Evolution, Function, and Assembly - Theory Meets Experiment |
Forschungszentrum - Jülich (Germany) |
| 10/06/2024 |
13/06/2024 |
3rd MOSBRI scientific conference 2024 |
Ljubljana (Slovenia) |
| 20/07/2024 |
26/07/2024 |
Gordon Research Seminar and Conference: Computational Chemistry 2024 |
University of Southern Maine - Portland, Maine (U.S.A.) |
Posters:
| Date |
Title |
Place |
File |
| 26/06/2019 |
Conformational analysis and rational design of tumor-associated altered peptide ligands |
Interdisciplinary Aspects of Biomolecular Modelling - Department of Biosciences - UniMi |
 |
| 21/06/2022 |
Accelerating SAXS intensities calculation of in-silico models |
EMBO: Small angle neutron and x-ray scattering from biomacromolecules in solution - European Photon and Neutron Science Campus - Grenoble (France) |
|
| 30/08/2023 |
An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for molecular simulations |
European Conference on Computational and Theoretical Chemistry (EuChemS CompChem 2023) - Olympic Museum - Thessaloniki (Greece) |
|
| 13/10/2023 |
Integrative modelling for the characterisation of the structure and dynamics of biomolecules |
UniMi PhD Workshop 2023 |
|
| 07/12/2023 |
Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations |
EMBO: Computational structural biology - EMBL Advanced Training Centre - Heidelberg (Germany) |
|
| 24/04/2024 |
Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations |
NIC Days: Biomolecular Evolution, Function, and Assembly - Theory Meets Experiment - Forschungszentrum - Jülich (Germany) |
|
| 23/07/2024 |
Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations |
University of Southern Maine - Portland, Maine (U.S.A.) |
|
Abroad experiences:
| Starting Date |
Ending Date |
Project |
Institution |
Supervisor |
| 07/05/2023 |
13/05/2023 |
Electron Paramagnetic Resonance / Double Electron-Electron Resonance spectroscopy |
CNRS - MOSBRI - Laboratoire de Bioenergetique et d'Ingenierie des Protéines - Marseille (France) |
Dr. Alessio Bonucci |
| 17/10/2023 |
19/10/2023 |
Short visit to "Center for Functional Protein Assemblies" and to "Bavarian NMR Center (BNMRZ)" |
Technische Universität München (Germany) |
Prof. Martin Zacharias |
| 12/09/2024 |
13/09/2024 |
Short visit to "Bavarian NMR Center (BNMRZ)" |
Technische Universität München (Germany) |
Prof. Michael Sattler |
Publications:
L- to D-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics Ballabio F., Broggini L., Paissoni C., Han X., Peqini K., Sala B.M., Sun R., Sandalova T., Barbiroli A., Achour A., Pellegrino S., Ricagno S., Camilloni C.
ACS Omega
Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol deliveryMilazzo F.M., Chaves-Sanjuan A., Minenkova O., Santapaola D., Anastasi A.M., Battistuzzi G., Chiapparino C., Rosi A., Merlo Pich E., Albertoni C., Marra E., Luberto L., Viollet C., Spagnoli L.G., Riccio A., Rossi A., Santoro M.G., Ballabio F., Paissoni C., Camilloni C., Bolognesi M., De Santis R.
Molecular Therapy
Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular SimulationsBallabio F., Paissoni C., Bollati M., de Rosa M., Capelli R., Camilloni C.
Journal of Chemical Theory and Computation
Calcium-Driven In Silico Inactivation of a Human Olfactory ReceptorPirona L., Ballabio F., Alfonso-Prieto M., Capelli R.
Journal of Chemical Information and Modeling
Nicotinic Acid Derivatives As Novel Noncompetitive α-Amylase and α-Glucosidase Inhibitors for Type 2 Diabetes Treatment Citarella A., Cavinato M., Rosini E., Shehi H., Ballabio F., Camilloni C., Fasano V., Silvani A., Passarella D., Pollegioni L., Nardini M.
ACS Medicinal Chemistry Letters
A missense mutation in the barley Xan-h gene encoding the Mg-chelatase subunit I leads to a viable pale green line with reduced daily transpiration rate Persello A., Tadini L., Rotasperti L., Ballabio F., Tagliani A., Torricella V., Jahns P., Dalal A., Moshelion M., Camilloni C., Rosignoli S., Hansson M., Cattivelli L., Horner D.S., Rossini L., Tondelli A., Salvi S., Pesaresi P.
Plant Cell Reports
