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 …

A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction

M Wang, L Kurgan, M Li - Briefings in Bioinformatics, 2023 - academic.oup.com
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 …

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 …

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 …

EpiTEAmDNA: Sequence feature representation via transfer learning and ensemble learning for identifying multiple DNA epigenetic modification types across species

F Li, S Liu, K Li, Y Zhang, M Duan, Z Yao, G Zhu… - Computers in Biology …, 2023 - Elsevier
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 …

[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 …

[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 …

[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 …

[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 …

MSTL-Kace: Prediction of Prokaryotic Lysine Acetylation Sites Based on Multistage Transfer Learning Strategy

GA Wang, X Yan, X Li, Y Liu, J Xia, X Zhu - ACS omega, 2023 - ACS Publications
As one of the most important post-translational modifications (PTM), lysine acetylation
(Kace) plays an important role in various biological activities. Traditional experimental …