Quality and bias of protein disorder predictors

TY - JOUR

T1 - Quality and bias of protein disorder predictors

AU - Nielsen, Jakob T.

AU - Mulder, Frans A.A.

PY - 2019/3/26

Y1 - 2019/3/26

N2 - Disorder in proteins is vital for biological function, yet it is challenging to characterize. Therefore, methods for predicting protein disorder from sequence are fundamental. Currently, predictors are trained and evaluated using data from X-ray structures or from various biochemical or spectroscopic data. However, the prediction accuracy of disordered predictors is not calibrated, nor is it established whether predictors are intrinsically biased towards one of the extremes of the order-disorder axis. We therefore generated and validated a comprehensive experimental benchmarking set of site-specific and continuous disorder, using deposited NMR chemical shift data. This novel experimental data collection is fully appropriate and represents the full spectrum of disorder. We subsequently analyzed the performance of 26 widely-used disorder prediction methods and found that these vary noticeably. At the same time, a distinct bias for over-predicting order was identified for some algorithms. Our analysis has important implications for the validity and the interpretation of protein disorder, as utilized, for example, in assessing the content of disorder in proteomes.

AB - Disorder in proteins is vital for biological function, yet it is challenging to characterize. Therefore, methods for predicting protein disorder from sequence are fundamental. Currently, predictors are trained and evaluated using data from X-ray structures or from various biochemical or spectroscopic data. However, the prediction accuracy of disordered predictors is not calibrated, nor is it established whether predictors are intrinsically biased towards one of the extremes of the order-disorder axis. We therefore generated and validated a comprehensive experimental benchmarking set of site-specific and continuous disorder, using deposited NMR chemical shift data. This novel experimental data collection is fully appropriate and represents the full spectrum of disorder. We subsequently analyzed the performance of 26 widely-used disorder prediction methods and found that these vary noticeably. At the same time, a distinct bias for over-predicting order was identified for some algorithms. Our analysis has important implications for the validity and the interpretation of protein disorder, as utilized, for example, in assessing the content of disorder in proteomes.

KW - BINDING

KW - BIOLOGICAL MACROMOLECULES

KW - CHEMICAL-SHIFTS

KW - DATABASE

KW - DISPROT

KW - DYNAMICS

KW - INTRINSIC DISORDER

KW - LARGE-SCALE ASSESSMENT

KW - P53

KW - REGION PREDICTIONS

UR - http://www.scopus.com/inward/record.url?scp=85063519519&partnerID=8YFLogxK

U2 - 10.1038/s41598-019-41644-w

DO - 10.1038/s41598-019-41644-w

M3 - Journal article

C2 - 30914747

AN - SCOPUS:85063519519

SN - 2045-2322

VL - 9

JO - Scientific Reports

JF - Scientific Reports

M1 - 5137

ER -