Improving protein succinylation sites prediction using embeddings from protein language model
Protein succinylation is an important post-translational modification (PTM) responsible for
many vital metabolic activities in cells, including cellular respiration, regulation, and repair …
many vital metabolic activities in cells, including cellular respiration, regulation, and repair …
LMPhosSite: a deep learning-based approach for general protein phosphorylation site prediction using embeddings from the local window sequence and pretrained …
Phosphorylation is one of the most important post-translational modifications and plays a
pivotal role in various cellular processes. Although there exist several computational tools to …
pivotal role in various cellular processes. Although there exist several computational tools to …
Analysis of Structural Changes in the Protein near the Phosphorylation Site
KS Nikolsky, LI Kulikova, DV Petrovskiy, VR Rudnev… - Biomolecules, 2023 - mdpi.com
Modification of the protein after synthesis (PTM) often affects protein function as supported
by numerous studies. However, there is no consensus about the degree of structural protein …
by numerous studies. However, there is no consensus about the degree of structural protein …
pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained …
Abstract Background Protein S-nitrosylation (SNO) plays a key role in transferring nitric
oxide-mediated signals in both animals and plants and has emerged as an important …
oxide-mediated signals in both animals and plants and has emerged as an important …
Post‐translational modifications of proteins in cardiovascular diseases examined by proteomic approaches
M Stastna - The FEBS Journal, 2024 - Wiley Online Library
Over 400 different types of post‐translational modifications (PTMs) have been reported and
over 200 various types of PTMs have been discovered using mass spectrometry (MS) …
over 200 various types of PTMs have been discovered using mass spectrometry (MS) …
DeepDN_iGlu: prediction of lysine glutarylation sites based on attention residual learning method and DenseNet.
J Jia, M Sun, G Wu, W Qiu - Mathematical Biosciences and …, 2022 - europepmc.org
As a key issue in orchestrating various biological processes and functions, protein post-
translational modification (PTM) occurs widely in the mechanism of protein's function of …
translational modification (PTM) occurs widely in the mechanism of protein's function of …
CaLMPhosKAN: Prediction of General Phosphorylation Sites in Proteins via Fusion of Codon Aware Embeddings with Amino Acid Aware Embeddings and Wavelet …
The mapping from codon to amino acid is surjective due to the high degeneracy of the
codon alphabet, suggesting that codon space might harbor higher information content …
codon alphabet, suggesting that codon space might harbor higher information content …
[HTML][HTML] Artificial intelligence and bioinformatics: a journey from traditional techniques to smart approaches
H Jamialahmadi, G Khalili-Tanha… - … from Bed to Bench, 2024 - pmc.ncbi.nlm.nih.gov
The incorporation of AI models into bioinformatics has brought about a revolutionary era in
the analysis and interpretation of biological data. This mini-review offers a succinct overview …
the analysis and interpretation of biological data. This mini-review offers a succinct overview …
SumoPred-PLM: human SUMOylation and SUMO2/3 sites Prediction using Pre-trained Protein Language Model
AV Palacios, P Acharya, AS Peidl… - NAR Genomics and …, 2024 - academic.oup.com
SUMOylation is an essential post-translational modification system with the ability to
regulate nearly all aspects of cellular physiology. Three major paralogues SUMO1, SUMO2 …
regulate nearly all aspects of cellular physiology. Three major paralogues SUMO1, SUMO2 …
NLP-based encoding techniques for prediction of post-translational modification sites and protein functions
With advancements in sequencing and proteomics approaches, computational functional
annotation of proteins is becoming increasingly crucial. Among these annotations, prediction …
annotation of proteins is becoming increasingly crucial. Among these annotations, prediction …