Prof. Dr. Paolo Carloni

 

Bioinformatics, Molecular Simulations, Free-Energy Calculations, Cellular Pathways Modeling

Expertise in computer simulation of molecular processes involved in neuronal function and
dysfunction and cancer progression.

 

Expertise

Development and application of computational methods in molecular medicine and
neurobiology. These include:

• Bioinformatics
• Molecular simulation: Ab-initio, classical and coarse grain Molecular Dynamics, hybrid methods
• Free-Energy calculations. Computational Spectroscopy and Mass Spec.
• Modeling of biological molecules and of cellular pathways

More details at the webpage.

 

Need

• Ligand synthesis
• In vitro/in cell/in vivo experiments
• Spectroscopy (e.g. NMR, CD, EXAFS) and Mass Spec.

 

References

1. J. Li, G. Rossetti, J. Dreyer, S. Raugei, E. Ippoliti, B. Lüscher, P. Carloni. Molecular simulation-based structural prediction of protein complexes in mass spectrometry: The human insulin dimer. PLoS Computational Biology, accepted for publication.
2. Nguyen T. H., G. Rossetti, F. Arnesano, E. Ippoliti, G. Natile, P. Carloni, Molecular recognition of platinated DNA from chromosomal HMGB1, Journal of Chemical Theory and Computation 2014. In press. doi: 10.1021/ct500402e
3. C. Zhang, D. Knyazev, Y. Vereshchaga, E. Ippoliti, T.H. Nguyen, P. Carloni, P. Pohl (2012) Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion. Proc. Natl. Acad. Sci, U.S.A. 109: 9744-9749.
4. A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional heteronuclear spectra of α-synuclein·dopamine adducts. Dibenedetto D, Rossetti G, Caliandro R, Carloni P. Biochemistry. 2013 Sep 24;52(38):6672-83.
5. Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes. Leguèbe M, Nguyen C, Capece L, Hoang Z, Giorgetti A, Carloni P. PLoS One. 2012;7(10):e47332. Epub 2012 Oct 19. PMID: 23094046