Modeling Lipid-Sterol Bilayers: Applications to Structural Evolution, Lateral Diffusion, and Rafts. - Martin J. Zuckermann; John H. Ipsen; Ling Miao; Ole G. Mouritsen; Morten Nielsen; James Polson; Jenifer Thewalt; Ilpo Vattulainen; Hong Zhu (Numerical Computer Methods, Part D, 2004)

Long-range interactions and parallel scalability in molecular simulations. - Michael Patra; Marja T. Hyvönen; Emma Falck; Mohsen Sabouri-Ghomi; Ilpo Vattulainen; Mikko Karttunen (Comput. Phys. Commun., 2007)

Assessing the Nature of Lipid Raft Membranes. - Perttu S. Niemelä; Samuli Ollila; Marja T. Hyvönen; Mikko Karttunen; Ilpo Vattulainen (PLoS Comput. Biol., 2007)

Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. - Pär Bjelkmar; Perttu S. Niemelä; Ilpo Vattulainen; Erik Lindahl (PLoS Comput. Biol., 2009)

Role of Lipids in Spheroidal High Density Lipoproteins. - Timo Vuorela; Andrea Catte; Perttu S. Niemelä; Anette Hall; Marja T. Hyvönen; Siewert J. Marrink; Mikko Karttunen; Ilpo Vattulainen (PLoS Comput. Biol., 2010)

Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations. - Artturi Koivuniemi; Timo Vuorela; Petri T. Kovanen; Ilpo Vattulainen; Marja T. Hyvönen (PLoS Comput. Biol., 2012)

How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations. - Tarja Äijänen; Artturi Koivuniemi; Matti Javanainen; Sami Rissanen; Tomasz Róg; Ilpo Vattulainen (PLoS Comput. Biol., 2014)

Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin. - Giray Enkavi; Heikki Mikkolainen; Burçin Güngör; Elina Ikonen; Ilpo Vattulainen (PLoS Comput. Biol., 2017)

Atomistic fingerprint of hyaluronan-CD44 binding. - Joni Vuorio; Ilpo Vattulainen; Hector Martinez-Seara (PLoS Comput. Biol., 2017)

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS. - Reinis Danne; Chetan S. Poojari; Hector Martinez-Seara; Sami Rissanen; Fabio Lolicato; Tomasz Róg; Ilpo Vattulainen (J. Chem. Inf. Model., 2017)

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling. - Tatu Pantsar; Sami Rissanen; Daniel Dauch; Tuomo Laitinen; Ilpo Vattulainen; Antti Poso (PLoS Comput. Biol., 2018)

Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions. - Matti Javanainen; Giray Enkavi; Ramon Guixà-González; Waldemar Kulig; Hector Martinez-Seara; Ilya Levental; Ilpo Vattulainen (PLoS Comput. Biol., 2019)

Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries. - Bart M. H. Bruininks; Tsjerk A. Wassenaar; Ilpo Vattulainen (J. Chem. Inf. Model., 2023)