title: Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins.
abstract: Intrinsically disordered proteins do not have stable secondary and/or tertiary structures but still function. More than 50 prediction methods have been developed and inherent relationships may be expected to exist among them. To investigate this, we conducted molecular simulations and algorithmic analyses on a minimal coarse-grained polypeptide model and discovered a common basis for the charge-hydropathy plot and packing-density algorithms that was verified by correlation analysis. The correlation analysis approach was applied to realistic datasets, which revealed correlations among some physical-chemical properties (charge-hydropathy plot, packing density, pairwise energy). The correlations indicated that these biophysical methods find a projected direction to discriminate ordered and disordered proteins. The optimized projection was determined and the ultimate accuracy limit of the existing algorithms is discussed.
authors: College of Chemistry and Molecular Engineering, Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China.
authors: Fan
authors: F
authors: Jin
authors: Zhirong
authors: Z
authors: Liu
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000378:metabolism; D000682:Amyloid / Q000737:chemistry; D055592:Biophysical Phenomena; D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D000682:Amyloid; D011506:Proteins