Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. - Michele Seeber; Angelo Felline; Francesco Raimondi 001; Stefanie Muff; Ran Friedman; Francesco Rao; Amedeo Caflisch; Francesca Fanelli (J. Comput. Chem., 2011)

Nucleotide Binding Switches the Information Flow in Ras GTPases. - Francesco Raimondi 001; Guillem Portella; Modesto Orozco; Francesca Fanelli (PLoS Comput. Biol., 2011)

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases. - Simona Mariani; Daniele Dell'Orco; Angelo Felline; Francesco Raimondi 001; Francesca Fanelli (PLoS Comput. Biol., 2013)

WebPSN: a web server for high-throughput investigation of structural communication in biomacromolecules. - Michele Seeber; Angelo Felline; Francesco Raimondi 001; Simona Mariani; Francesca Fanelli (Bioinform., 2015)

Catching Functional Modes and Structural Communication in Dbl Family Rho Guanine Nucleotide Exchange Factors. - Francesco Raimondi 001; Angelo Felline; Francesca Fanelli (J. Chem. Inf. Model., 2015)

Interconnecting Flexibility, Structural Communication, and Function in RhoGEF Oncoproteins. - Angelo Felline; Luca Belmonte; Francesco Raimondi 001; Luca Bellucci; Francesca Fanelli (J. Chem. Inf. Model., 2019)

PRECOG: PREdicting COupling probabilities of G-protein coupled receptors. - Gurdeep Singh; Asuka Inoue; J. Silvio Gutkind; Robert B. Russell; Francesco Raimondi 001 (Nucleic Acids Res., 2019)

Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces. - Francesco Raimondi 001; Joshua G. Burkhart; Matthew J. Betts; Robert B. Russell; Guanming Wu (F1000Research, 2021)

PRECOGx: exploring GPCR signaling mechanisms with deep protein representations. - Marin Matic; Gurdeep Singh; Francesco Carli; Natalia De Oliveira Rosa; Pasquale Miglionico; Lorenzo Magni; J. Silvio Gutkind; Robert B. Russell; Asuka Inoue; Francesco Raimondi 001 (Nucleic Acids Res., 2022)

Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. - Joshua G. Burkhart; Guanming Wu; Xubo Song; Francesco Raimondi 001; Shannon K. McWeeney; Melissa H. Wong; Youping Deng (Patterns, 2023)