biostudies-literatureUnknown13(2)Emperador AWe study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the absence of dissociation events. We also find that TIP4P/2005 is the only water model that reproduces the fast association/dissociation dynamics of ubiquitin and best identifies its binding surface. Our results show the critical role of the water model in the description of protein-protein interactions and binding.PolymersE176https://www.ebi.ac.uk/biostudies/studies/S-EPMC7825341biostudies-literatureEffect of the Water Model in Simulations of Protein-Protein Recognition and Association.PMC7825341Crehuet RGuardia EEmperador AfalseEffect of the Water Model in Simulations of Protein-Protein Recognition and Association.We study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the absence of dissociation events. We also find that TIP4P/2005 is the only water model that reproduces the fast association/dissociation dynamics of ubiquitin and best identifies its binding surface. Our results show the critical role of the water model in the description of protein-protein interactions and binding.2021-01-01T00:00:00Z2021 Jan2025-04-27T00:43:54.205Z2021-02-21T01:55:00ZS-EPMC78253413341900810.3390/polym13020176