Leveraging transformers‐based language models in proteome bioinformatics
NQK Le - Proteomics, 2023 - Wiley Online Library
In recent years, the rapid growth of biological data has increased interest in using
bioinformatics to analyze and interpret this data. Proteomics, which studies the structure …
bioinformatics to analyze and interpret this data. Proteomics, which studies the structure …
A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction
Human leukocyte antigen class I (HLA-I) molecules bind intracellular peptides produced by
protein hydrolysis and present them to the T cells for immune recognition and response …
protein hydrolysis and present them to the T cells for immune recognition and response …
CollagenTransformer: end-to-end transformer model to predict thermal stability of collagen triple helices using an NLP approach
E Khare, C Gonzalez-Obeso, DL Kaplan… - ACS Biomaterials …, 2022 - ACS Publications
Collagen is one of the most important structural proteins in biology, and its structural
hierarchy plays a crucial role in many mechanically important biomaterials. Here, we …
hierarchy plays a crucial role in many mechanically important biomaterials. Here, we …
Prediction of antioxidant peptides using a quantitative structure− activity relationship predictor (AnOxPP) based on bidirectional long short-term memory neural …
D Qin, L Jiao, R Wang, Y Zhao, Y Hao… - Computers in Biology and …, 2023 - Elsevier
Antioxidant peptides can protect against free radical-mediated diseases, especially food-
derived antioxidant peptides are considered as potential competitors among synthetic …
derived antioxidant peptides are considered as potential competitors among synthetic …
EpiTEAmDNA: Sequence feature representation via transfer learning and ensemble learning for identifying multiple DNA epigenetic modification types across species
Methylation is a major DNA epigenetic modification for regulating the biological processes
without altering the DNA sequence, and multiple types of DNA methylations have been …
without altering the DNA sequence, and multiple types of DNA methylations have been …
[HTML][HTML] Fusing sequence and structural knowledge by heterogeneous models to accurately and interpretively predict drug–target affinity
X Zeng, KY Zhong, B Jiang, Y Li - Molecules, 2023 - mdpi.com
Drug–target affinity (DTA) prediction is crucial for understanding molecular interactions and
aiding drug discovery and development. While various computational methods have been …
aiding drug discovery and development. While various computational methods have been …
[HTML][HTML] CapsNet-MHC predicts peptide-MHC class I binding based on capsule neural networks
M Kalemati, S Darvishi, S Koohi - Communications Biology, 2023 - nature.com
Abstract The Major Histocompatibility Complex (MHC) binds to the derived peptides from
pathogens to present them to killer T cells on the cell surface. Developing computational …
pathogens to present them to killer T cells on the cell surface. Developing computational …
[HTML][HTML] IUP-BERT: identification of umami peptides based on BERT features
L Jiang, J Jiang, X Wang, Y Zhang, B Zheng, S Liu… - Foods, 2022 - mdpi.com
Umami is an important widely-used taste component of food seasoning. Umami peptides are
specific structural peptides endowing foods with a favorable umami taste. Laboratory …
specific structural peptides endowing foods with a favorable umami taste. Laboratory …
[HTML][HTML] ACPPfel: Explainable deep ensemble learning for anticancer peptides prediction based on feature optimization
M Liu, T Wu, X Li, Y Zhu, S Chen, J Huang… - Frontiers in …, 2024 - frontiersin.org
Background: Cancer is a significant global health problem that continues to cause a high
number of deaths worldwide. Traditional cancer treatments often come with risks that can …
number of deaths worldwide. Traditional cancer treatments often come with risks that can …
MSTL-Kace: Prediction of Prokaryotic Lysine Acetylation Sites Based on Multistage Transfer Learning Strategy
As one of the most important post-translational modifications (PTM), lysine acetylation
(Kace) plays an important role in various biological activities. Traditional experimental …
(Kace) plays an important role in various biological activities. Traditional experimental …