Millisecond-scale molecular dynamics simulations on Anton. - David E. Shaw; Ron O. Dror; John K. Salmon; J. P. Grossman; Kenneth M. Mackenzie; Joseph A. Bank; Cliff Young; Martin M. Deneroff; Brannon Batson; Kevin J. Bowers; Edmond Chow; Michael P. Eastwood; et al. (SC, 2009)

PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure. - Wouter Boomsma; Jes Frellsen; Tim Harder; Sandro Bottaro; Kristoffer E. Johansson; Pengfei Tian; Kasper Stovgaard; Christian Andreetta; Simon Olsson; Jan B. Valentin; Lubomir D. Antonov; Anders S. Christensen; et al. (J. Comput. Chem., 2013)

Combining Experiments and Simulations Using the Maximum Entropy Principle. - Wouter Boomsma; Jesper Ferkinghoff-Borg; Kresten Lindorff-Larsen (PLoS Comput. Biol., 2014)

Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops. - Gaetano Invernizzi; Matteo Tiberti; Matteo Lambrughi; Kresten Lindorff-Larsen; Elena Papaleo (PLoS Comput. Biol., 2014)

ENCORE: Software for Quantitative Ensemble Comparison. - Matteo Tiberti; Elena Papaleo; Tone Bengtsen; Wouter Boomsma; Kresten Lindorff-Larsen (PLoS Comput. Biol., 2015)

An automatic seating plan algorithm. - Kresten Lindorff-Larsen (PeerJ Prepr., 2018)

Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts. - Ramon Crehuet; Pedro J. Buigues; Xavier Salvatella; Kresten Lindorff-Larsen (Entropy, 2019)

What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? - James S. Fraser; Kresten Lindorff-Larsen; Massimiliano Bonomi (J. Chem. Inf. Model., 2020)

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution. - Andreas Haahr Larsen; Yong Wang 056; Sandro Bottaro; Sergei Grudinin; Lise Arleth; Kresten Lindorff-Larsen (PLoS Comput. Biol., 2020)

Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase. - Yong Wang 056; Kresten Lindorff-Larsen (Zenodo, 2020)

DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. - Giulio Tesei; João M. Martins; Micha B. A. Kunze; Yong Wang; Ramon Crehuet; Kresten Lindorff-Larsen (PLoS Comput. Biol., 2021)

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. - Samuel E. Hoff; F. Emil Thomasen; Kresten Lindorff-Larsen; Massimiliano Bonomi (PLoS Comput. Biol., 2024)

Optimized Protein-Excipient Interactions in the Martini 3 Force Field. - Tobias M. Prass; Kresten Lindorff-Larsen; Patrick Garidel; Michaela Blech; Lars V. Schäfer (J. Chem. Inf. Model., 2025)

Zero-shot protein stability prediction by inverse folding models: a free energy interpretation. - Jes Frellsen; Maher M. Kassem; Tone Bengtsen; Lars Olsen; Kresten Lindorff-Larsen; Jesper Ferkinghoff-Borg; Wouter Boomsma (CoRR, 2025)