A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing

2021 ◽  
Author(s):  
Shiliang Li ◽  
Chaoqian Cai ◽  
Jiayu Gong ◽  
Xiaofeng Liu ◽  
Honglin Li
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Protein Function ◽  
Protein Function Prediction ◽  
Drug Repurposing ◽  
Function Prediction ◽  
Protein Binding Site

Mask blast with a new chemical logic of amino acids for improved protein function prediction

2021 ◽  
Author(s):  
Amita Pathak ◽  
Toran Roy ◽  
Avinash Edubilli ◽  
Bhyravabhotla Jayaram
Keyword(s):  
Amino Acids ◽  
Protein Function ◽  
Protein Function Prediction ◽  
Function Prediction

scholarly journals DeepGOPlus: improved protein function prediction from sequence

2021 ◽  
Author(s):  
Maxat Kulmanov ◽  
Robert Hoehndorf
Keyword(s):  
Protein Function ◽  
Protein Function Prediction ◽  
Function Prediction

scholarly journals Functional homology between the yeast regulatory proteins GAL4 and LAC9: LAC9-mediated transcriptional activation in Kluyveromyces lactis involves protein binding to a regulatory sequence homologous to the GAL4 protein-binding site.

1987 ◽  
Vol 7 (12) ◽  
pp. 4400-4406 ◽  
Author(s):  
K D Breunig ◽  
P Kuger
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Transcriptional Activation ◽  
Kluyveromyces Lactis ◽  
Regulatory Protein ◽  
Binding Activity ◽  
Protein Binding Site ◽  
Regulatory Sequence ◽  
Functional Homology ◽  
Beta Galactosidase

As shown previously, the beta-galactosidase gene of Kluyveromyces lactis is transcriptionally regulated via an upstream activation site (UASL) which contains a sequence homologous to the GAL4 protein-binding site in Saccharomyces cerevisiae (M. Ruzzi, K.D. Breunig, A.G. Ficca, and C.P. Hollenberg, Mol. Cell. Biol. 7:991-997, 1987). Here we demonstrate that the region of homology specifically binds a K. lactis regulatory protein. The binding activity was detectable in protein extracts from wild-type cells enriched for DNA-binding proteins by heparin affinity chromatography. These extracts could be used directly for DNase I and exonuclease III protection experiments. A lac9 deletion strain, which fails to induce the beta-galactosidase gene, did not contain the binding factor. The homology of LAC9 protein with GAL4 (J.M. Salmeron and S. A. Johnston, Nucleic Acids Res. 14:7767-7781, 1986) strongly suggests that LAC9 protein binds directly to UASL and plays a role similar to that of GAL4 in regulating transcription.

scholarly journals ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network

Molecules ◽  
2017 ◽  
Vol 22 (10) ◽  
pp. 1732 ◽  
Author(s):  
Renzhi Cao ◽  
Colton Freitas ◽  
Leong Chan ◽  
Miao Sun ◽  
Haiqing Jiang ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Translation ◽  
Recurrent Neural Network ◽  
Protein Function ◽  
Protein Function Prediction ◽  
Function Prediction ◽  
Neural Machine Translation
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