Prediction of Ligand Induced Folding Regions from Protein Sequences
Date Issued
2007
Date
2007
Author(s)
Fan, Yu-Sheng
DOI
zh-TW
Abstract
In many eukaryotes, more and more proteins have been founded to be fully or partially disordered, which means unstable three-dimensional conformation. In particular, most of these disordered proteins, also called intrinsically unstructured proteins (IUPs), are shown to be functionally significant. When IUPs interact with their partners, they usually undergo disorder-to-order transition that turns the disordered regions into stable structures. This process is also referred to as "induced folding".
Although there has been an increasing amount of studies on IUPs, few datasets are provided for analysis and investigation on induced folding. Since the “induced folding” regions of IUPs are closely related to the protein functions, correctly predicting these regions facilitates the studies in proteomics. In this thesis, we collect a ligand induced folding benchmark from PDB (Protein Data Bank), and propose a predictor for detecting ligand induced folding regions directly from protein sequences.
The benchmark is built with the PDB structures that contain proteins with identical sequences but inconsistent structure information. Each pair of structures is manually confirmed that the dissimilar regions are spatially close to ligands within 5Å. Furthermore, a prediction model is built with feature sets based on position-specific scoring matrices (PSSM). The developed Radial Based Function Network classifier (using QuickRBF package) achieves an AUC score (area under the ROC) of 0.7833. After expanding the feature sets with physiochemical and predicted secondary structure information, the prediction performance can be further improved to 0.8142.
Subjects
蛋白質
非穩定區段
序列
二級結構
觸發蛋白質折疊
protein
disorder region
SSE
sequence analysis
disorder
induced folding
Type
thesis
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