Phosphorylation plays a key role in plant biology, such as the accumulation of plant cells to form the observed proteome. Statistical analysis found that many phosphorylation sites are located in disordered regions. However, current force fields are mainly trained for structural proteins, which might not have the capacity to perfectly capture the dynamic conformation of the phosphorylated proteins. Therefore, we evaluated the performance of , a balanced force field between structural and disordered proteins, for the sampling of the phosphorylated proteins. The test results of 11 different phosphorylated systems, including dipeptides, disordered proteins, folded proteins, and their complex, indicate that the force field can better sample the conformations of phosphorylation sites for disordered proteins and disordered regions than . For the solvent model, the results strongly suggest that the force field with the water model is the best combination for the conformer sampling. Additional tests of and force fields on two phosphorylated systems suggest that the overall performance of is similar to that of and better than that of . These results can help other researchers to choose suitable force field and solvent models to investigate the dynamic properties of phosphorylation proteins.
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| http://dx.doi.org/10.3390/ijms231911285 | DOI Listing |
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