O-GlcNAc informatics: advances and trends
As a post-translational modification, protein glycosylation is critical in health and disease. O-
Linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), as an …
Linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), as an …
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 …
PEL-PVP: Application of plant vacuolar protein discriminator based on PEFT ESM-2 and bilayer LSTM in an unbalanced dataset
Plant vacuoles, play a crucial role in maintaining cellular stability, adapting to environmental
changes, and responding to external pressures. The accurate identification of vacuolar …
changes, and responding to external pressures. The accurate identification of vacuolar …
LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model
Motivation Recent advancements in natural language processing have highlighted the
effectiveness of global contextualized representations from protein language models (pLMs) …
effectiveness of global contextualized representations from protein language models (pLMs) …
Recurrent neural network-based prediction of O-GlcNAcylation sites in mammalian proteins
P Seber, RD Braatz - Computers & Chemical Engineering, 2024 - Elsevier
O-GlcNAcylation has the potential to be an important target for therapeutics, but a motif or an
algorithm to reliably predict O-GlcNAcylation sites is not available. Current predictive models …
algorithm to reliably predict O-GlcNAcylation sites is not available. Current predictive models …
Prediction of inhibitory peptides against E. coli with desired MIC value
In the past, several methods have been developed for predicting antibacterial and
antimicrobial peptides, but only limited attempts have been made to predict their minimum …
antimicrobial peptides, but only limited attempts have been made to predict their minimum …
Benchmarking text-integrated protein language model embeddings and embedding fusion on diverse downstream tasks
YS Ko, J Parkinson, W Wang - bioRxiv, 2024 - biorxiv.org
Protein language models (pLMs) have traditionally been trained in an unsupervised manner
using large protein sequence databases with an autoregressive or masked-language …
using large protein sequence databases with an autoregressive or masked-language …
pLM-DBPs: Enhanced DNA-Binding Protein Prediction in Plants Using Embeddings From Protein Language Models
S Pokharel, K Barasa, P Pratyush, DB KC - bioRxiv, 2024 - biorxiv.org
DNA-binding proteins (DBPs) in plants play critical roles in gene regulation, development,
and environmental response. While various machine learning and deep learning models …
and environmental response. While various machine learning and deep learning models …
Deep-Learning Uncovers certain CCM Isoforms as Transcription Factors
BACKGROUND: Cerebral Cavernous Malformations (CCMs) are brain vascular
abnormalities associated with an increased risk of hemorrhagic strokes. Familial CCMs …
abnormalities associated with an increased risk of hemorrhagic strokes. Familial CCMs …