Ou YY - Search Results

1

MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks.

Malik MS, Chang YY, Liu YC, Le VT, Ou YY. Malik MS, et al. Among authors: ou yy. J Chem Inf Model. 2024 Aug 12. doi: 10.1021/acs.jcim.4c00961. Online ahead of print. J Chem Inf Model. 2024. PMID: 39133248

2

ProtTrans and multi-window scanning convolutional neural networks for the prediction of protein-peptide interaction sites.

Le VT, Zhan ZJ, Vu TT, Malik MS, Ou YY. Le VT, et al. Among authors: ou yy. J Mol Graph Model. 2024 Jul;130:108777. doi: 10.1016/j.jmgm.2024.108777. Epub 2024 Apr 17. J Mol Graph Model. 2024. PMID: 38642500

3

Deciphering the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence Modeling.

Liu YC, Lin YJ, Chang YY, Chuang CC, Ou YY. Liu YC, et al. Among authors: ou yy. J Mol Biol. 2024 Nov 15;436(22):168769. doi: 10.1016/j.jmb.2024.168769. Epub 2024 Aug 29. J Mol Biol. 2024. PMID: 39214282

4

VesiMCNN: Using pre-trained protein language models and multiple window scanning convolutional neural networks to identify vesicular transport proteins.

Le VT, Tseng YH, Liu YC, Malik MS, Ou YY. Le VT, et al. Among authors: ou yy. Int J Biol Macromol. 2024 Sep 26;280(Pt 3):136048. doi: 10.1016/j.ijbiomac.2024.136048. Online ahead of print. Int J Biol Macromol. 2024. PMID: 39332561

5

DeepNeoAG: Neoantigen epitope prediction from melanoma antigens using a synergistic deep learning model combining protein language models and multi-window scanning convolutional neural networks.

Chuang CC, Liu YC, Ou YY. Chuang CC, et al. Among authors: ou yy. Int J Biol Macromol. 2024 Nov;281(Pt 1):136252. doi: 10.1016/j.ijbiomac.2024.136252. Epub 2024 Oct 2. Int J Biol Macromol. 2024. PMID: 39366619

6

Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs.

Le NQ, Ou YY. Le NQ, et al. Among authors: ou yy. BMC Bioinformatics. 2016 Jul 30;17:298. doi: 10.1186/s12859-016-1163-x. BMC Bioinformatics. 2016. PMID: 27475771 Free PMC article.

7

Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins.

Le NQ, Ho QT, Ou YY. Le NQ, et al. Among authors: ou yy. J Comput Chem. 2017 Sep 5;38(23):2000-2006. doi: 10.1002/jcc.24842. Epub 2017 Jun 22. J Comput Chem. 2017. PMID: 28643394

8

DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters.

Taju SW, Nguyen TT, Le NQ, Kusuma RMI, Ou YY. Taju SW, et al. Among authors: ou yy. Bioinformatics. 2018 Sep 15;34(18):3111-3117. doi: 10.1093/bioinformatics/bty302. Bioinformatics. 2018. PMID: 29668844

9

Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks.

Le NQ, Ho QT, Ou YY. Le NQ, et al. Among authors: ou yy. Anal Biochem. 2018 Aug 15;555:33-41. doi: 10.1016/j.ab.2018.06.011. Epub 2018 Jun 13. Anal Biochem. 2018. PMID: 29908156

10

Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins.

Le NQK, Ho QT, Ou YY. Le NQK, et al. Among authors: ou yy. J Bioinform Comput Biol. 2019 Feb;17(1):1950005. doi: 10.1142/S0219720019500057. J Bioinform Comput Biol. 2019. PMID: 30866734

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