Massimiliano Bonomi

Massimiliano Bonomi serves as a Structure Manager and Principal Investigator at the Pasteur Institute in Paris, leading multiple research projects at the intersection of computational biology, structural biology, and biophysics. His research group focuses on integrative modeling approaches combining computational methods with experimental data, particularly in the areas of RNA structure and dynamics, protein dynamics with cryo-EM, and molecular simulation analysis.

Dr. Bonomi's research spans computational structural biology with emphasis on developing and applying advanced modeling techniques to understand biomolecular systems. His work integrates machine learning, Bayesian statistics, and parallel computing to tackle challenges in RNA-small molecule interactions, protein conformational dynamics, and structural virology. The research has significant implications for drug discovery, particularly in developing computational approaches for RNA-targeted therapeutics and understanding viral pathogenesis mechanisms.

Analysis of Dr. Bonomi's recent publications reveals a strong trend toward integrative computational approaches that combine multiple experimental techniques with advanced simulation methods. His work increasingly incorporates artificial intelligence and machine learning techniques to analyze complex biomolecular systems, with particular focus on RNA structure prediction, protein-protein interactions, and membrane transporter dynamics. The research demonstrates consistent progression from method development to biological applications, with growing emphasis on practical drug discovery applications.

Dr. Bonomi actively mentors several PhD students and postdoctoral researchers including Matteo Marengo, Francesco Righini, and Francesco Panei. His research is supported through multiple project grants including 'Targeting RNA structure and dynamics with small molecules' and 'Integrative modelling of protein structure and dynamics with cryo-EM', with additional funding for software development projects like PLUMED and PLUMED-NEST.

Dr. Bonomi leads the development of several important computational resources including PLUMED (an open-source library for free-energy calculations), HARIBOSS (a database of RNA-small molecules structures), and PLUMED-NEST (a public repository for reproducing simulation results). These tools form the foundation of his research team's work and are widely used by the international computational biology community.