Three-dimensional computation of atom depth in complex molecular structures. - Daniele Varrazzo; Andrea Bernini; Ottavia Spiga; Arianna Ciutti; Stefano Chiellini; Vincenzo Venditti; Luisa Bracci; Neri Niccolai (Bioinform., 2005)

ProCoCoA: A quantitative approach for analyzing protein core composition. - Silvia Bottini; Andrea Bernini; Matteo De Chiara; Diego Garlaschelli; Ottavia Spiga; Marco Dioguardi; Elisa Vannuccini; Anna Tramontano; Neri Niccolai (Comput. Biol. Chem., 2013)

Toward a generalized computational workflow for exploiting transient pockets as new targets for small molecule stabilizers: Application to the homogentisate 1, 2-dioxygenase mutants at the base of rare disease Alkaptonuria. - Andrea Bernini; Silvia Galderisi; Ottavia Spiga; Giulia Bernardini 003; Neri Niccolai; Fabrizio Manetti; Annalisa Santucci (Comput. Biol. Chem., 2017)

Glycine-induced formation and druggability score prediction of protein surface pockets. - Pietro Bongini; Neri Niccolai; Monica Bianchini (J. Bioinform. Comput. Biol., 2019)

A deep attention network for predicting amino acid signals in the formation of α-helices. - Anna Visibelli; Pietro Bongini; Alberto Rossi; Neri Niccolai; Monica Bianchini (J. Bioinform. Comput. Biol., 2020)

Structural bioinformatics survey on disease-inducing missense mutations. - Pietro Bongini; Simone Gardini; Monica Bianchini; Ottavia Spiga; Neri Niccolai (J. Bioinform. Comput. Biol., 2021)

Structural Bioinformatic Survey of Protein-Small Molecule Interfaces Delineates the Role of Glycine in Surface Pocket Formation. - Pietro Bongini; Neri Niccolai; Alfonso Trezza; Guido Mangiavacchi; Annalisa Santucci; Ottavia Spiga; Monica Bianchini; Simone Gardini (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

A Discrete Geometry Method for Atom Depth Computation in Complex Molecular Systems. - Sara Marziali; Giacomo Nunziati; Alessia Lucia Prete; Neri Niccolai; Sara Brunetti; Monica Bianchini (DGMM, 2024)

SADIC v2: A modern implementation of the Simple Atom Depth Index Calculator. - Sara Marziali; Giacomo Nunziati; Alessia Lucia Prete; Neri Niccolai; Monica Bianchini (SoftwareX, 2024)