Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data. - Hamed Khakzad; Lotta Happonen; Johan Malmström; Lars Malmström (Bioinform., 2021)

Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology. - Hamed Khakzad; Lotta Happonen; Yasaman Karami; Sounak Chowdhury; Gizem Ertürk Bergdahl; Michael Nilges; Guy Tran Van Nhieu; Johan Malmström; Lars Malmström (PLoS Comput. Biol., 2021)

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics. - Carlos Gueto-Tettay; Di Tang; Lotta Happonen; Moritz Heusel; Hamed Khakzad; Johan Malmström; Lars Malmström (PLoS Comput. Biol., 2023)