Binding-Induced Folding of a Natively Unstructured Transcription Factor. - Adrian Gustavo Turjanski; J. Silvio Gutkind; Robert B. Best; Gerhard Hummer (PLoS Comput. Biol., 2008)

Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. - Edina Rosta; H. Lee Woodcock III; Bernard R. Brooks; Gerhard Hummer (J. Comput. Chem., 2009)

Convergence and error estimation in free energy calculations using the weighted histogram analysis method. - Fangqiang Zhu; Gerhard Hummer (J. Comput. Chem., 2012)

Membrane-Elasticity Model of Coatless Vesicle Budding Induced by ESCRT Complexes. - Bartosz Rózycki; Evzen Boura; James H. Hurley; Gerhard Hummer (PLoS Comput. Biol., 2012)

Nobel 2013 Chemistry: Methods for computational chemistry. - Walter Thiel; Gerhard Hummer (Nat., 2013)

Interface-Resolved Network of Protein-Protein Interactions. - Margaret E. Johnson; Gerhard Hummer (PLoS Comput. Biol., 2013)

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics. - Christoph Dellago; Gerhard Hummer (Entropy, 2014)

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. - Pilar Cossio; David Rohr; Fabio Baruffa; Markus Rampp; Volker Lindenstruth; Gerhard Hummer (Comput. Phys. Commun., 2017)

Scaffolding the cup-shaped double membrane in autophagy. - Amir Houshang Bahrami; Mary G. Lin; Xuefeng Ren; James H. Hurley; Gerhard Hummer (PLoS Comput. Biol., 2017)

Classical Molecular Dynamics with Mobile Protons. - Themis Lazaridis; Gerhard Hummer (J. Chem. Inf. Model., 2017)

Computational epitope map of SARS-CoV-2 spike protein. - Mateusz Sikora; Sören von Bülow; Florian E. C. Blanc; Michael Gecht; Roberto Covino; Gerhard Hummer (PLoS Comput. Biol., 2021)

Machine-guided path sampling to discover mechanisms of molecular self-organization. - Hendrik Jung; Roberto Covino; A. Arjun; Christian Leitold; Christoph Dellago; Peter G. Bolhuis; Gerhard Hummer (Nat. Comput. Sci., 2023)

Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. - Sören von Bülow; Mateusz Sikora; Florian E. C. Blanc; Roberto Covino; Gerhard Hummer (PLoS Comput. Biol., 2023)

Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. - Carsten Kutzner; Vedran Miletic; Karen Palacio Rodríguez; Markus Rampp; Gerhard Hummer; Bert L. de Groot; Helmut Grubmüller (J. Comput. Chem., 2025)

asyncmd: A python library to orchestrate complex molecular dynamics simulation campaigns on high performance computing systems. - Hendrik Jung; Gerhard Hummer (J. Open Source Softw., 2025)