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 …

Machine intelligence in peptide therapeutics: A next‐generation tool for rapid disease screening

S Basith, B Manavalan, T Hwan Shin… - Medicinal research …, 2020 - Wiley Online Library
Discovery and development of biopeptides are time‐consuming, laborious, and dependent
on various factors. Data‐driven computational methods, especially machine learning (ML) …

Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations

P Das, T Sercu, K Wadhawan, I Padhi… - Nature Biomedical …, 2021 - nature.com
The de novo design of antimicrobial therapeutics involves the exploration of a vast chemical
repertoire to find compounds with broad-spectrum potency and low toxicity. Here, we report …

ToxinPred 3.0: An improved method for predicting the toxicity of peptides

AS Rathore, S Choudhury, A Arora, P Tijare… - Computers in Biology …, 2024 - Elsevier
Toxicity emerges as a prominent challenge in the design of therapeutic peptides, causing
the failure of numerous peptides during clinical trials. In 2013, our group developed …

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 …

Recent progress in the discovery and design of antimicrobial peptides using traditional machine learning and deep learning

J Yan, J Cai, B Zhang, Y Wang, DF Wong, SWI Siu - Antibiotics, 2022 - mdpi.com
Antimicrobial resistance has become a critical global health problem due to the abuse of
conventional antibiotics and the rise of multi-drug-resistant microbes. Antimicrobial peptides …

Benchmarking of different molecular docking methods for protein-peptide docking

P Agrawal, H Singh, HK Srivastava, S Singh… - BMC …, 2019 - Springer
Background Molecular docking studies on protein-peptide interactions are a challenging
and time-consuming task because peptides are generally more flexible than proteins and …

AMPGAN v2: machine learning-guided design of antimicrobial peptides

CM Van Oort, JB Ferrell, JM Remington… - Journal of chemical …, 2021 - ACS Publications
Antibiotic resistance is a critical public health problem. Each year∼ 2.8 million resistant
infections lead to more than 35 000 deaths in the US alone. Antimicrobial peptides (AMPs) …

Glial connexins and pannexins in the healthy and diseased brain

C Giaume, CC Naus, JC Sáez… - Physiological …, 2021 - journals.physiology.org
Over the past several decades a large amount of data have established that glial cells, the
main cell population in the brain, dynamically interact with neurons and thus impact their …

An overview of in silico vaccine design against different pathogens and cancer

K Kardani, A Bolhassani, A Namvar - Expert Review of Vaccines, 2020 - Taylor & Francis
Introduction Due to overcome the hardness of the vaccine design, computational
vaccinology is emerging widely. Prediction of T cell and B cell epitopes, antigen processing …