This project contains the code to implement KinasePhos 3.0, if you use any of this code, please cite: "Ma, Renfei, Shangfu Li, Wenshuo Li, Lantian Yao, Hsien-Da Huang, and Tzong-Yi Lee. "KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites." bioRxiv (2021)." ************************************ Folders ****************************************** ********* ./data: 1.Family K-S sites: Original data of experimentally verified kinase-specific phosphorylation sites at family level 2.Family positive: Experimentally verified kinase-specific phosphorylation sites extracted from 1. 3.Family negative: All the same types of residues in phosphorylated substrate proteins of a family, except those known to be positive phosphorylation sites, were regarded as negative data of that kinase family. . . . The same goes with the data at individual kinase level and group level. !!!It should be noted that CD-HIT and CD-HIT-2D were adopted to reduce data similarity. ********* ./features: This folder contains the features of positive and negative data encoded with BLOSUM62, the data were clustered at group, family, and individual kinase level. For family and individual kinase level, S/T/Y, S/T and Y sites were considered separately. ********* ./pretrained XGBoost models This folder contains the pretrained XGBoost models of KinasePhos 3.0 ********* ./results This folder contains the performance of all models resulting from using 10-fold cross-validation ************************************ Files ****************************************** ~~~~~~~~~ ./1_data preprocessing.ipynb This file precesses the original data in the "./data" folder, gets the positive and negative data, and saves them in "./data" ~~~~~~~~~ ./2_feature extraction_BLOSUM62.ipynb This file encodes the positive and negative data in "./data" and saves the encoded features to "./features" !!!It is recommended for users to implement CD-HIT-2D and/or CD-HIT to reduce data similarity, otherwise the size of negative data is too large ~~~~~~~~~ ./3_models.ipynb This file develops the machine learning-based models of KinasePhos 3.0 ~~~~~~~~~ "./family 15.npy": list of kinase families with experimentally verified kinase-specific phosphorylation S/T/Y sites more than 15 "./family_st 15.npy": list of kinase families with experimentally verified kinase-specific phosphorylation S/T sites more than 15 "./family_y 15.npy": list of kinase families with experimentally verified kinase-specific phosphorylation Y sites more than 15 "./kinase 15.npy": list of kinases with experimentally verified kinase-specific phosphorylation S/T/Y sites more than 15 "./kinase_st 15.npy": list of kinases with experimentally verified kinase-specific phosphorylation S/T sites more than 15 "./kinase_y 15.npy": list of kinases with experimentally verified kinase-specific phosphorylation Y sites more than 15 ************************************ Zip file ****************************************** ./KinasePhosApp.zip This is the standalone tool of KinasePhos3.0, which is supported by Windows.