DeepSite: protein-binding site predictor using 3D-convolutional neural networks.
作者： J Jiménez , S Doerr , G Martínez-Rosell , A S Rose , G De Fabritiis
DOI: 10.1093/BIOINFORMATICS/BTX350
关键词:
摘要: … -art convolutional neural networks, where the algorithm is learned by examples. In total, 7622 proteins … We treat protein structures from a computer vision perspective, as if they were 3D …
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sci-hub.se 参考文章(20)
G. Patrick Brady Jr., Pieter F.W. Stouten, Fast prediction and visualization of protein binding pockets with PASS. Journal of Computer-aided Molecular Design. ,vol. 14, pp. 383- 401 ,(2000) , 10.1023/A:1008124202956
Snehalata Dongre, Rushi Longadge, Class Imbalance Problem in Data Mining Review arXiv: Learning. ,(2013)
Yoshua Bengio, Practical recommendations for gradient-based training of deep architectures Neural Networks: Tricks of the Trade (2nd ed.). pp. 437- 478 ,(2012) , 10.1007/978-3-642-35289-8_26
Jérémy Desaphy, Guillaume Bret, Didier Rognan, Esther Kellenberger, sc-PDB: a 3D-database of ligandable binding sites—10 years on Nucleic Acids Research. ,vol. 43, pp. 399- 404 ,(2015) , 10.1093/NAR/GKU928
Jérémy Desaphy, Karima Azdimousa, Esther Kellenberger, Didier Rognan, Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes Journal of Chemical Information and Modeling. ,vol. 52, pp. 2287- 2299 ,(2012) , 10.1021/CI300184X
Martin Weisel, Ewgenij Proschak, Gisbert Schneider, PocketPicker: analysis of ligand binding-sites with shape descriptors Chemistry Central Journal. ,vol. 1, pp. 7- 7 ,(2007) , 10.1186/1752-153X-1-7
Manfred Hendlich, Friedrich Rippmann, Gerhard Barnickel, LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins Journal of Molecular Graphics & Modelling. ,vol. 15, pp. 359- 363 ,(1997) , 10.1016/S1093-3263(98)00002-3
David G. Levitt, Leonard J. Banaszak, POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids Journal of Molecular Graphics. ,vol. 10, pp. 229- 234 ,(1992) , 10.1016/0263-7855(92)80074-N
D. Comaniciu, P. Meer, Mean shift: a robust approach toward feature space analysis IEEE Transactions on Pattern Analysis and Machine Intelligence. ,vol. 24, pp. 603- 619 ,(2002) , 10.1109/34.1000236
Alexander S. Rose, Peter W. Hildebrand, NGL Viewer: a web application for molecular visualization Nucleic Acids Research. ,vol. 43, pp. 576- ,(2015) , 10.1093/NAR/GKV402