CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology. - Alessandro Paiardini; Francesco Bossa; Stefano Pascarella (Nucleic Acids Res., 2005)

PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL. - Emanuele Bramucci; Alessandro Paiardini; Francesco Bossa; Stefano Pascarella (BMC Bioinform., 2012)

PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL. - Giacomo Janson; Chengxin Zhang; Maria Giulia Prado; Alessandro Paiardini (Bioinform., 2017)

Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling. - Giacomo Janson; Alessandro Grottesi; Marco Pietrosanto; Gabriele Ausiello; Giulia Guarguaglini; Alessandro Paiardini (PLoS Comput. Biol., 2019)

PyMod 3: a complete suite for structural bioinformatics in PyMOL. - Giacomo Janson; Alessandro Paiardini (Bioinform., 2021)

DockingPie: a consensus docking plugin for PyMOL. - Serena Rosignoli; Alessandro Paiardini (Bioinform., 2022)

A Deep Neural Network for G-Quadruplexes Binding Proteins Classification. - Francesco Di Luzio; Alessandro Paiardini; Federica Colonnese; Antonello Rosato; Massimo Panella (IWANN (1), 2023)

PyPCN: protein contact networks in PyMOL. - Serena Rosignoli; Luisa di Paola; Alessandro Paiardini (Bioinform., 2023)