Integration of molecular docking analysis and molecular dynamics simulations for studying food proteins and bioactive peptides

A Vidal-Limon, JE Aguilar-Toalá… - Journal of agricultural …, 2022 - ACS Publications
In silico tools, such as molecular docking, are widely applied to study interactions and
binding affinity of biological activity of proteins and peptides. However, restricted sampling of …

Review and perspective on bioactive peptides: A roadmap for research, development, and future opportunities

Z Du, Y Li - Journal of Agriculture and Food Research, 2022 - Elsevier
Bioactive peptides (BPs) possess a broad spectrum of beneficial effects, such as antioxidant,
antihypertensive, antidiabetic, anticancer, anti-inflammatory, antimicrobial, and anti-aging …

UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity

Z Du, X Ding, Y Xu, Y Li - Briefings in Bioinformatics, 2023 - academic.oup.com
Identification of potent peptides through model prediction can reduce benchwork in wet
experiments. However, the conventional process of model buildings can be complex and …

BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides

P Charoenkwan, C Nantasenamat, MM Hasan… - …, 2021 - academic.oup.com
Motivation The identification of bitter peptides through experimental approaches is an
expensive and time-consuming endeavor. Due to the huge number of newly available …

StackIL6: a stacking ensemble model for improving the prediction of IL-6 inducing peptides

P Charoenkwan, W Chiangjong… - Briefings in …, 2021 - academic.oup.com
The release of interleukin (IL)-6 is stimulated by antigenic peptides from pathogens as well
as by immune cells for activating aggressive inflammation. IL-6 inducing peptides are …

Strengths and limitations of in silico tools to assess physicochemical properties, bioactivity, and bioavailability of food-derived peptides

F Rivero-Pino, MC Millan-Linares… - Trends in Food Science …, 2023 - Elsevier
Background Bioactive peptides obtained from different food sources have been proved to
exert several bioactivities, such as antioxidant, antihypertensive, antimicrobial, or anti …

Advances in machine learning screening of food bioactive compounds

Y Zhang, X Bao, Y Zhu, Z Dai, Q Shen, Y Xue - Trends in Food Science & …, 2024 - Elsevier
Background Food contains abundant bioactive compounds that play a crucial role in human
health. However, conventional methods for screening food bioactive compounds (FBCs) are …

DeepIPs: comprehensive assessment and computational identification of phosphorylation sites of SARS-CoV-2 infection using a deep learning-based approach

H Lv, FY Dao, H Zulfiqar, H Lin - Briefings in Bioinformatics, 2021 - academic.oup.com
The rapid spread of SARS-CoV-2 infection around the globe has caused a massive health
and socioeconomic crisis. Identification of phosphorylation sites is an important step for …

AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning

P Charoenkwan, S Ahmed, C Nantasenamat… - Scientific reports, 2022 - nature.com
Amyloid proteins have the ability to form insoluble fibril aggregates that have important
pathogenic effects in many tissues. Such amyloidoses are prominently associated with …

ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism

L Wei, X Ye, Y Xue, T Sakurai… - Briefings in Bioinformatics, 2021 - academic.oup.com
Motivation: Peptides have recently emerged as promising therapeutic agents against
various diseases. For both research and safety regulation purposes, it is of high importance …