AIMC Topic: Protein Processing, Post-Translational

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Improved prediction of post-translational modification crosstalk within proteins using DeepPCT.

Bioinformatics (Oxford, England) Nov 28, 2024
MOTIVATION: Post-translational modification (PTM) crosstalk events play critical roles in biological processes. Several machine learning methods have been developed to identify PTM crosstalk within proteins, but the accuracy is still far from satisfa...
Computational Biology Protein Processing, Post-Translational Algorithms Proteins Databases, Protein Deep Learning Neural Networks, Computer
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Sitetack: a deep learning model that improves PTM prediction by using known PTMs.

Bioinformatics (Oxford, England) Nov 1, 2024
MOTIVATION: Post-translational modifications (PTMs) increase the diversity of the proteome and are vital to organismal life and therapeutic strategies. Deep learning has been used to predict PTM locations. Still, limitations in datasets and their ana...
Software Algorithms Humans Neural Networks, Computer Proteome Protein Processing, Post-Translational Databases, Protein Deep Learning Proteomics
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DeepPRMS: advanced deep learning model to predict protein arginine methylation sites.

Briefings in functional genomics Jul 19, 2024
Protein methylation is a form of post-translational modifications of protein, which is crucial for various cellular processes, including transcription activity and DNA repair. Correctly predicting protein methylation sites is fundamental for research...
Neural Networks, Computer Algorithms Humans Protein Processing, Post-Translational Proteins Methylation Deep Learning Computational Biology Arginine
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TransPTM: a transformer-based model for non-histone acetylation site prediction.

Briefings in bioinformatics Mar 27, 2024
Protein acetylation is one of the extensively studied post-translational modifications (PTMs) due to its significant roles across a myriad of biological processes. Although many computational tools for acetylation site identification have been develo...
Acetylation Computational Biology Protein Processing, Post-Translational Proteins Databases, Protein Software Algorithms Humans Neural Networks, Computer
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Lactylation prediction models based on protein sequence and structural feature fusion.

Briefings in bioinformatics Jan 22, 2024
Lysine lactylation (Kla) is a newly discovered posttranslational modification that is involved in important life activities, such as glycolysis-related cell function, macrophage polarization and nervous system regulation, and has received widespread ...
Protein Processing, Post-Translational Amino Acid Sequence Lysine Natural Language Processing Protein Domains
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Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences.

Database : the journal of biological databases and curation Jan 19, 2024
The post-translational modifications occur as crucial molecular regulatory mechanisms utilized to regulate diverse cellular processes. Malonylation of proteins, a reversible post-translational modification of lysine/k residues, is linked to a variety...
Machine Learning Deep Learning Proteins Lysine Protein Processing, Post-Translational
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THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model.

Bioinformatics (Oxford, England) Nov 1, 2023
MOTIVATION: Quantitative determination of protein thermodynamic stability is a critical step in protein and drug design. Reliable prediction of protein stability changes caused by point variations contributes to developing-related fields. Over the pa...
Deep Learning Protein Processing, Post-Translational Proteins Neural Networks, Computer Software
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PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk.

Briefings in bioinformatics Mar 19, 2023
Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk...
Protein Processing, Post-Translational Protein Domains Neural Networks, Computer Proteome Signal Transduction
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FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites.

Briefings in bioinformatics Nov 19, 2022
Glutarylation is a post-translational modification which plays an irreplaceable role in various functions of the cell. Therefore, it is very important to accurately identify the glutarylation substrates and its corresponding glutarylation sites. In r...
Support Vector Machine Protein Processing, Post-Translational Algorithms Computational Biology Amino Acids Supervised Machine Learning
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PLP_FS: prediction of lysine phosphoglycerylation sites in protein using support vector machine and fusion of multiple F_Score feature selection.

Briefings in bioinformatics Sep 20, 2022
A newly invented post-translational modification (PTM), phosphoglycerylation, has shown its essential role in the construction and functional properties of proteins and dangerous human diseases. Hence, it is very urgent to know about the molecular me...
Protein Processing, Post-Translational Humans Computational Biology Amino Acid Sequence Algorithms Lysine Support Vector Machine Proteins
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