HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. - Jaroslav Bendl; Jan Stourac; Eva Sebestova; Ondrej Vavra; Milos Musil; Jan Brezovsky; Jirí Damborský (Nucleic Acids Res., 2016)

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. - Jaroslav Bendl; Milos Musil; Jan Stourac; Jaroslav Zendulka; Jirí Damborský; Jan Brezovsky (PLoS Comput. Biol., 2016)

FireProt: web server for automated design of thermostable proteins. - Milos Musil; Jan Stourac; Jaroslav Bendl; Jan Brezovsky; Zbynek Prokop; Jaroslav Zendulka; Tomás Martínek; David Bednar; Jirí Damborský (Nucleic Acids Res., 2017)

FireProtDB: database of manually curated protein stability data. - Jan Stourac; Juraj Dubrava; Milos Musil; Jana Horackova; Jirí Damborský; Stanislav Mazurenko; David Bednar (Nucleic Acids Res., 2021)

FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. - Milos Musil; Andrej Jezik; Jana Horackova; Simeon Borko; Petr Kabourek; Jirí Damborský; David Bednar (Briefings Bioinform., 2023)

Anticipating protein evolution with successor sequence predictor. - Rayyan T. Khan; Pavel Kohout; Milos Musil; Monika Rosinska; Jirí Damborský; Stanislav Mazurenko; David Bednar (J. Cheminformatics, 2025)