FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites

Qiao, Ning; Qi, Zedong; Wang, Yue; Deng, Ansheng; Chen, Chen

doi:10.1093/bib/bbac421

Cited by 5 publications

(2 citation statements)

References 29 publications

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“…Our results indicate that features from CKSAAP and DDE were the most contributing for two models (Figure A,D) and the second most contributing in the other two models (Figure B,C). It is known that CKSAAP features can capture patterns of short linear motif information and thereby preserve the coevolutionary information of amino acid residues because of which they are employed in post-translational modification site identification. − …”

Section: Resultsmentioning

confidence: 99%

NRPreTo: A Machine Learning-Based Nuclear Receptor and Subfamily Prediction Tool

et al. 2023

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The nuclear receptor (NR) superfamily includes phylogenetically related ligand-activated proteins, which play a key role in various cellular activities. NR proteins are subdivided into seven subfamilies based on their function, mechanism, and nature of the interacting ligand. Developing robust tools to identify NR could give insights into their functional relationships and involvement in disease pathways. Existing NR prediction tools only use a few types of sequence-based features and are tested on relatively similar independent datasets; thus, they may suffer from overfitting when extended to new genera of sequences. To address this problem, we developed Nuclear Receptor Prediction Tool (NRPreTo), a two-level NR prediction tool with a unique training approach where in addition to the sequence-based features used by existing NR prediction tools, six additional feature groups depicting various physiochemical, structural, and evolutionary features of proteins were utilized. The first level of NRPreTo allows for the successful prediction of a query protein as NR or non-NR and further subclassifies the protein into one of the seven NR subfamilies in the second level. We developed Random Forest classifiers to test on benchmark datasets, as well as the entire human protein datasets from RefSeq and Human Protein Reference Database (HPRD). We observed that using additional feature groups improved the performance. We also observed that NRPreTo achieved high performance on the external datasets and predicted 59 novel NRs in the human proteome. The source code of NRPreTo is publicly available at .

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Section: Resultsmentioning

confidence: 99%

NRPreTo: A Machine Learning-Based Nuclear Receptor and Subfamily Prediction Tool

et al. 2023

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“…4B and 4C). It is known that CKSAAP features can capture patterns of short linear motif information and thereby preserve the coevolutionary information of amino acid residues because of which they are employed in post-translational modification site identification [45][46][47] .…”

Section: Analysis Of the Importance Of Protein Feature Categoriesmentioning

confidence: 99%

NRPreTo: A Machine Learning Based Nuclear Receptor and Subfamily Prediction Tool

Madugula

Pandey

Amalapurapu

et al. 2022

Preprint

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The Nuclear Receptor (NR) superfamily includes phylogenetically related ligand-activated proteins, which play a key role in various cellular activities. NR proteins are subdivided into seven subfamilies based on their function, mechanism, and nature of the interacting ligand. Developing robust tools to identify NR could give insights into their functional relationships and involvement in disease pathways. Existing NR prediction tools only use a few types of sequence-based features and are tested on relatively similar independent datasets; thus, they may suffer from overfitting when extended to new genera of sequences. To address this problem, we developed Nuclear Receptor Prediction Tool (NRPreTo); a two-level NR prediction tool with a unique training approach where in addition to the sequence-based features used by existing NR prediction tools, six additional feature groups depicting various physiochemical, structural and evolutionary features of proteins were utilized. The first level of NRPreTo allows for the successful prediction of a query protein as NR or non-NR, and further subclassifies the protein into one of the seven NR subfamilies in the second level. We developed Random Forest classifiers to test on benchmark datasets, as well as the entire human protein datasets from RefSeq and Human Protein Reference Database (HPRD). We observed that using additional feature groups improved performance. We also observed that NRPreTo achieved high performance on the external datasets and predicted 59 novel NRs in the human proteome. The source code of NRPreTo is publicly available at https://github.com/bozdaglab/NRPreTo.

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Emerging trends in post-translational modification: Shedding light on Glioblastoma multiforme

Kumari,

Gupta,

Ambasta

et al. 2023

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer

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FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites

Cited by 5 publications

References 29 publications

NRPreTo: A Machine Learning-Based Nuclear Receptor and Subfamily Prediction Tool

NRPreTo: A Machine Learning-Based Nuclear Receptor and Subfamily Prediction Tool

NRPreTo: A Machine Learning Based Nuclear Receptor and Subfamily Prediction Tool

Emerging trends in post-translational modification: Shedding light on Glioblastoma multiforme

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