Our prediction tool, DeepATP, combines evolutionary information in the form of Position Specific Scoring Matrix and two-dimensional Convolutional Neural Network to predict ATP-binding sites in membrane proteins with an MCC of 0.89 and an AUC of 99%. Compared to recently published ATP-binding site ...
Correctly identifying the protein-ATP binding site is valuable for both protein function annotation and new drug discovery. However, the number of non-ATP-binding residues is much more than the number of ATP-binding residues, which makes the prediction a classical imbalanced learning problem. ...
Consequently developing computational methods for protein-ATP binding residues prediction has a great potential application. Despite the importance of the relevant research, little work was reported in this regard. Raghava et al.[39] has done some significant work on protein-ATP binding sites ...
Rao, B., Yu, X., Bai, J., & Hu, J. (2023). E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.3c01298IF: 5.6Q1 Data and code: https://github.c...
ATPbindingprediction ATPbinding is a sequence-based prediction method for protein-ATP binding sites prediction with deep convolutional neural network and ensemble learning. Two predictors are developed including a Residual-inception-based predictor and a Multi-inception-based predictor. The predicton result...
(2023). E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding. Journal of Chemical Information and Modeling. doi.org/10.1021/acs.jci 5.6 Q1 B2 Data and code: github.com/jun-csbio/e2 —完— 关注我,记得标星哦～...
et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). Article ADS PubMed Central PubMed Google Scholar Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta. Crystallogr. D Biol. Crystallogr. 66, 486–...
‘dorsal fin’16,32. The crystallography analysis16indicated that ATP binding causes rearrangement of the ‘head’, ‘right flipper’, and ‘dorsal fin’ domains (Fig.2A,B). These conformational changes occur both around the ligand (ATP) binding site and between subunits16,33. Thus, the ...
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment Bioinformatics, 28 (15) (2012), pp. 2074-2075 CrossrefView in ScopusGoogle Scholar [24] D.S. Cao, N. Xiao, Q.S. Xu, A.F. Chen Rcpi: R/Bioconductor package to generate various descri...
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