Francesco Pontiggia

Cyberinfrastructure Research Consultant
Francesco graduated from SISSA/ISAS in Trieste - Italy, where he designed and applied statistical tools to model protein dynamics. He then worked as Postdoctoral Associate at Brandeis University, where he conducted research on functional conformational transitions in bacterial signaling proteins and protein kinases.
At Brandeis University he went on to work as a research computing specialist, managing the research computing cluster and supporting researchers in the Division of Science. Francesco joined the Research Computing team in May 2017.


  • Pontiggia, F., Zen, A. and Micheletti, C., 2008. Small-and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics. Biophysical journal95(12), pp.5901-5912.
  • Zorba, A., Buosi, V., Kutter, S., Kern, N., Pontiggia, F., Cho, Y.J. and Kern, D., 2014. Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2. Elife3, p.e02667.
  • Potestio, R., Pontiggia, F. and Micheletti, C., 2009. Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. Biophysical journal96(12), pp.4993-5002.
  • Kerns, S.J., Agafonov, R.V., Cho, Y.J., Pontiggia, F., Otten, R., Pachov, D.V., Kutter, S., Phung, L.A., Murphy, P.N., Thai, V. and Alber, T., 2015. The energy landscape of adenylate kinase during catalysis. Nature structural & molecular biology22(2), p.124.
  • Pontiggia, F., Colombo, G., Micheletti, C. and Orland, H., 2007. Anharmonicity and self-similarity of the free energy landscape of protein G. Physical review letters98(4), p.048102.
  • Aleksiev, T., Potestio, R., Pontiggia, F., Cozzini, S. and Micheletti, C., 2009. PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains. Bioinformatics25(20), pp.2743-2744.
  • Pontiggia, F., Pachov, D.V., Clarkson, M.W., Villali, J., Hagan, M.F., Pande, V.S. and Kern, D., 2015. Free energy landscape of activation in a signalling protein at atomic resolution. Nature communications6, p.7284.
  • Potestio, R., Aleksiev, T., Pontiggia, F., Cozzini, S. and Micheletti, C., 2010. ALADYN: a web server for aligning proteins by matching their large-scale motion. Nucleic acids research38(suppl_2), pp.W41-W45.
  • Capozzi, F., Luchinat, C., Micheletti, C. and Pontiggia, F., 2007. Essential dynamics of helices provide a functional classification of EF-hand proteins. Journal of proteome research6(11), pp.4245-4255.
  • Carnevale, V., Pontiggia, F. and Micheletti, C., 2007. Structural and dynamical alignment of enzymes with partial structural similarity. 
  • Villali, J., Pontiggia, F., Clarkson, M.W., Hagan, M.F. and Kern, D., 2014. Evidence against the “Y–T coupling” mechanism of activation in the response regulator NtrC. Journal of molecular biology426(7), pp.1554-1567.
  • Chakrabarti, K.S., Agafonov, R.V., Pontiggia, F., Otten, R., Higgins, M.K., Schertler, G.F., Oprian, D.D. and Kern, D., 2016. Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis. Cell reports14(1), pp.32-42.
  • Pontiggia, F., 2008. Protein structure and functionally-oriented dynamics: from atomistic to coarse-grained models (Doctoral dissertation).
  •  Carnevale, V., Micheletti, C., Pontiggia, F. and Potestio, R., 2011. Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins. In Multiscale Approaches to Protein Modeling (pp. 159-178). Springer, New York, NY.
  • Pontiggia, F., Pachov, D.V., Clarkson, M.W., Villali, J., Hagan, M.F., Pande, V.S. and Kern, D., 2015. Activation Mechanism of a Signaling Protein at Atomic Resolution. Biophysical Journal108(2), p.376a.
  • Potestio, R., Pontiggia, F., Aleksiev, T., Cozzini, S. and Micheletti, C., 2010. Pisqrd: A Novel Variational Scheme to Identify Dinamical Domains in Proteins. Biophysical Journal98(3), p.237a.