Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. - Fotis A. Baltoumas; Margarita C. Theodoropoulou; Stavros J. Hamodrakas (J. Comput. Aided Mol. Des., 2016)

A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils. - Nikolaos N. Louros; Fotis A. Baltoumas; Stavros J. Hamodrakas; Vassiliki A. Iconomidou (J. Comput. Aided Mol. Des., 2016)

Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1). - Kostas A. Triantaphyllopoulos; Fotis A. Baltoumas; Stavros J. Hamodrakas (J. Comput. Aided Mol. Des., 2019)

The gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields. - Fotis A. Baltoumas; Stavros J. Hamodrakas; Vassiliki A. Iconomidou (J. Comput. Chem., 2019)

VICTOR: A visual analytics web application for comparing cluster sets. - Evangelos Karatzas; Maria Gkonta; Joana Hotova; Fotis A. Baltoumas; Panagiota I. Kontou; Christopher J. Bobotsis; Pantelis G. Bagos; Georgios A. Pavlopoulos (Comput. Biol. Medicine, 2021)

Arena3Dweb: interactive 3D visualization of multilayered networks. - Evangelos Karatzas; Fotis A. Baltoumas; Nikolaos A. Panayiotou; Reinhard Schneider 002; Georgios A. Pavlopoulos (Nucleic Acids Res., 2021)

Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters. - Fotis A. Baltoumas; Evangelos Karatzas; David Páez-Espino; Nefeli K. Venetsianou; Eleni Aplakidou; Anastasis Oulas; Robert D. Finn; Sergey Ovchinnikov; Evangelos Pafilis; Nikos Kyrpides; Georgios A. Pavlopoulos (Frontiers Bioinform., 2023)

Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources. - Evangelos Karatzas; Fotis A. Baltoumas; Eleni Aplakidou; Panagiota I. Kontou; Panos Stathopoulos; Leonidas Stefanis; Pantelis G. Bagos; Georgios A. Pavlopoulos (Bioinform., 2023)