ArticlePolymers2021
Effect of the Water Model in Simulations of Protein-Protein Recognition and Association.
Article in Polymers, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Design and synthesis of novel thiazole/1,2,4-triazole/quinoline hybrids as antiproliferative agents, apoptosis inducers, immunomodulators, and multi-EGFR/BRAFMolecular diversity · 2026Article
- Evaluating Force Matching as a Parametrization Strategy for the CHARMM36m Force Field Using Phosphorylation.The journal of physical chemistry. B · 2026Article
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- Design, synthesis, and antiproliferative activity of new 5-ethylsulfonyl-indazole-3-carbohydrazides as dual EGFR/VEGFR-2 kinases inhibitors.Journal of enzyme inhibition and medicinal chemistry · 2025Article
- Article
- Extending the PARCH Scale: Assessing Hydropathy of Proteins across Multiple Water Models.Journal of chemical information and modeling · 2025Article
- The Influence of Ionic Environment on Nucleosome-Mica Interactions Revealed via Molecular Dynamics Simulations.The journal of physical chemistry. B · 2024Article
- Impact of water models on the structure and dynamics of enzyme tunnels.Computational and structural biotechnology journal · 2024Article
- Advanced sampling simulations of coupled folding and binding of phage P22 N-peptide to boxB RNA.Biophysical journal · 2024Article
- The Influence of Ionic Environment on Nucleosome-Mica Interactions Revealed via Molecular Dynamics Simulations.bioRxiv : the preprint server for biology · 2024Article
- PACSAB Server: A Web-Based Tool for the Study of Aggregation and the Conformational Ensemble of Disordered and Folded Proteins.International journal of molecular sciences · 2024Article
- (Non)Resonance Bonds in Molecular Dynamics Simulations: A Case Study concerning CEntropy (Basel, Switzerland) · 2024Article
- Article
- Lessons Learned from Multiobjective Automatic Optimizations of Classical Three-Site Rigid Water Models Using Microscopic and Macroscopic Target Experimental Observables.Journal of chemical and engineering data · 2023Article
- Identification of Novel Cannabinoid CB2 Receptor Agonists from Botanical Compounds and Preliminary Evaluation of Their Anti-Osteoporotic Effects.Molecules (Basel, Switzerland) · 2022Article
- Accurate Description of Protein-Protein Recognition and Protein Aggregation with the Implicit-Solvent-Based PACSAB Protein Model.Polymers · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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