title: A method for WD40 repeat detection and secondary structure prediction.
abstract: WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction.
authors.affiliation: Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, PR China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Wang
authors.forename: Fan
authors.initials: F
authors.lastname: Jiang
authors.forename: Zhu
authors.initials: Z
authors.lastname: Zhuo
authors.forename: Xian-Hui
authors.initials: XH
authors.lastname: Wu
authors.forename: Yun-Dong
authors.initials: YD
authors.lastname: Wu
mesh_terms: D000818:Animals; D030562:Databases, Protein; D006801:Humans; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: C494421:LRRN1 protein, human; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D011506:Proteins