g_permute: Permutation-reduced phase space density compaction. - Friedemann Reinhard; Oliver F. Lange; Jochen S. Hub; Jürgen Haas; Helmut Grubmüller (Comput. Phys. Commun., 2009)

Detection of Functional Modes in Protein Dynamics. - Jochen S. Hub; Bert L. de Groot (PLoS Comput. Biol., 2009)

Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation. - Jochen S. Hub; Marcus B. Kubitzki; Bert L. de Groot (PLoS Comput. Biol., 2010)

MemGen: a general web server for the setup of lipid membrane simulation systems. - Christopher J. Knight; Jochen S. Hub (Bioinform., 2015)

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics. - Christopher J. Knight; Jochen S. Hub (Nucleic Acids Res., 2015)

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics. - Roman Shevchuk; Jochen S. Hub (PLoS Comput. Biol., 2017)

Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase. - Massimiliano Anselmi; Paolo Calligari; Jochen S. Hub; Marco Tartaglia; Gianfranco Bocchinfuso; Lorenzo Stella (J. Chem. Inf. Model., 2020)

Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy. - Jeremy Lapierre; Jochen S. Hub (J. Chem. Inf. Model., 2023)

Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations. - Alejandro Martínez León; Benjamin Ries; Jochen S. Hub; Aniket Magarkar (J. Cheminformatics, 2025)