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Federico Fogolari

Associate Professor Applied Physics

Contacts

Dipartimento di Scienze Matematiche, Informatiche e Fisiche (DMIF)
Universita' di Udine
Via delle Scienze 206
33100 Udine - Italy
Tel ++39 0432 558493 Fax ++39 0432 558499
E-mail federico.fogolari(at)uniud.it

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Short CV

  • Name (first name, family name): Federico Fogolari
  • Place and date of birth: Udine (Italy), 7 May 1963

Professional experience

  • 11/2004 - now Associate Professor of Applied Physics in the Department of Mathematics, Informatics and Physics (formerly at the Department of Biomedical Sciences and Technologies) of the University of Udine (Italy).
  • 7/2007 visiting scholar at the University of Utrecht (The Netherlands) in the laboratory of prof. A. Bonvin.11/1989 - 6/1990 Biophysical Chemistry Laboratory of the University of Nijmegen (The Netherlands) (director prof. C. W. Hilbers)
  • 4/1997 - 11/2004 Assistant Professor in Organic Chemistry at Scientic and Technological Department in the Faculty of Sciences at the University of Verona (Italy), in the group of Prof. H. Molinari.
  • 10/1995 - 9/1996 University of California at San Diego in the research group of prof. McCammon, supported by a NATO fellowship.
  • 5/1992 - 8/1992 European Molecular Biology Laboratory, (EMBL) Heidelberg (Germany), in the group of A. Pastore, supported by a short term EMBO fellowship.
  • 2/1991 - 3/1997 Department of Biomedical Sciences and Technologies of the University of Udine (Italy), in the group of Prof. P. Viglino and Dr. G. Esposito.

Education

  • 1992 Philosophiae Doctor, International School for Advanced Studies (SISSA/ISAS) in Trieste (Italy), Biophysics sector (Director: prof. A. Borsellino) (supervisors dr. G. Esposito and prof. P. Viglino).
  • 1990 Magister Philosophiae, International School for Advanced Studies (SISSA/ISAS) in Trieste (Italy), Biophysics sector (Director: prof. A. Borsellino) (supervisors dr. F. van de Ven and prof. A. Borsellino).
  • 1982 - 1988 University in Trieste (Italy), Degree in Physics, with mark 110/110 cum laude (Supervisor: prof. G. Manzini)

 

Research interests

  • Electrostatics in biomolecular and nanoscale systems
  • Computer simulations of biomolecules,
  • Structural bioinformatics
  • Entropy calculations in biomolecular systems.

 

Teaching

  • Courses in NMR, statistics, physics, bioinformatics, biopolymer structure and dynamics for Biotechnology degree and in PhD schools in Milan, Padua, Udine.

He's currently teaching the following courses at the University of Udine:

  • Biological Physical Chemistry for the Biotechnology bachelor degree
  • Principles of Drug Design for the Biotechnology bachelor degree
  • Quantum Computing and Communication for the Cybersecurity and Artificial Intellgence master degree

 

Scientific and editorial activity

  • Author of ca. 150 ISI publications.
  • Author of 8 structures deposited in the Protein Data Bank.
  • Formerly Associate Editor of BMC Structural Biology
  • Editorial board of: International Journal of Molecular Science (Molecular Informatics).
  • Associate Editor of Frontiers in Molecular Biosciences (Biological Modeling and Simulation).

 

Selected recent publications and link to complete list

  • S.S.M Mahmoud, B. Portelli, G. D’Agostino, G. Pollastri, G. Serra, F. Fogolari. A comparison between mutual information, linear models and deep learning networks for protein secondary structure prediction. Curr. Bioinformatics, in press, 2023
  • M.A. Soler, O. Ozkilinc, Y. Hunashal, P. Giannozzi, G. Esposito, F. Fogolari. Molecular electrostatics and pKa shifts calculations with the Generalized Born model. A tutorial through examples with Bluues2. Comp. Phys. Comm. 287, 108716, 2023
  • R. Borelli, A. Dovier, F Fogolari. Data Structures and Algorithms for k-th Nearest Neighbours Conformational Entropy Estimation. Biophysica 2, 340-352, 2022
  • F Fogolari, G Esposito, B Tidor. Entropy of Two-Molecule Correlated Translational-Rotational Motions Using the kth Nearest Neighbor Method. J. Chem. Theory Comput. 17, 3039-3051, 2021
  • F Fogolari, G Esposito. Optimal Relabeling of Water Molecules and Single-Molecule Entropy Estimation. Biophysica 1, 279-296, 2021
  • S.S.M Mahmoud, G Esposito, G. Serra, F. Fogolari. Generalized Born radii computation using linear models and neural networks. Bioinformatics, 36, 1757-1764, 2020.
  • F Fogolari, A Corazza, G Esposito. Free energy, enthalpy and entropy from implicit solvent end-point simulations. Front. Mol. Biosci. 5, 11, 2018
  • F Fogolari, O Maloku, CJ Dongmo Foumthuim, A Corazza, G Esposito. PDB2ENTROPY and PDB2TRENT: Conformational and Translational–Rotational Entropy from Molecular Ensembles. J. Chem. Inform. Model. 58 (7), 1319-1324, 2018
  • F Fogolari, CJ Dongmo Foumthuim, S Fortuna, MA Soler, A Corazza, G. Esposito. Accurate Estimation of the Entropy of Rotation–Translation Probability Distributions. J. Chem. Theory Comput. 12, 1-8, 2016
  • F Fogolari, A Corazza, S Fortuna, MA Soler, B VanSchouwen, G Brancolini, S Corni, G Melacini, G Esposito. Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.. PloS one 10 (7), e0132356, 2015.

Complete list with bibliometric data