Name
Abstract | ||
|---|---|---|
The earliest whole protein order/disorder predictor (Uversky et al., Proteins, 41: 415-427 (2000)), herein called the charge-hydropathy (C-H) plot, was originally developed using the Kyte-Doolittle (1982) hydropathy scale (Kyte & Doolittle., J. Mol. Biol, 157: 105-132(1982)). Here the goal is to determine whether the performance of the C-H plot in separating structured and disordered proteins can be improved by using an alternative hydropathy scale.Using the performance of the CH-plot as the metric, we compared 19 alternative hydropathy scales, with the finding that the Guy (1985) hydropathy scale (Guy, Biophys. J, 47:61-70(1985)) was the best of the tested hydropathy scales for separating large collections structured proteins and intrinsically disordered proteins (IDPs) on the C-H plot. Next, we developed a new scale, named IDP-Hydropathy, which further improves the discrimination between structured proteins and IDPs. Applying the C-H plot to a dataset containing 109 IDPs and 563 non-homologous fully structured proteins, the Kyte-Doolittle (1982) hydropathy scale, the Guy (1985) hydropathy scale, and the IDP-Hydropathy scale gave balanced two-state classification accuracies of 79%, 84%, and 90%, respectively, indicating a very substantial overall improvement is obtained by using different hydropathy scales. A correlation study shows that IDP-Hydropathy is strongly correlated with other hydropathy scales, thus suggesting that IDP-Hydropathy probably has only minor contributions from amino acid properties other than hydropathy.We suggest that IDP-Hydropathy would likely be the best scale to use for any type of algorithm developed to predict protein disorder. |
Year | DOI | Venue |
|---|---|---|
2014 | 10.1186/1471-2105-15-S17-S4 | BMC Bioinformatics |
Keywords | Field | DocType |
Intrinsically disordered proteins, natively unstructured or unfolded proteins, structure and disorder prediction, support vector machines | Biology,Amino acid,Intrinsically disordered proteins,Bioinformatics,DNA microarray,Disorder classification | Journal |
Volume | Issue | ISSN |
15 Suppl 17 | S-17 | 1471-2105 |
Citations | PageRank | References |
3 | 0.69 | 20 |
Authors | ||
10 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Fei Huang | 1 | 21 | 8.57 |
| Christopher J Oldfield | 2 | 87 | 9.54 |
| Bin Xue | 3 | 76 | 5.71 |
| Wei-Lun Hsu | 4 | 32 | 4.14 |
| Jingwei Meng | 5 | 6 | 3.12 |
| Xiaowen Liu | 6 | 3 | 0.69 |
| Li Shen | 7 | 3 | 0.69 |
| Pedro Romero | 8 | 76 | 10.73 |
| Vladimir N Uversky | 9 | 166 | 13.43 |
| A. Keith Dunker | 10 | 466 | 77.54 |