A comprehensive survey on deep graph representation learning

W Ju, Z Fang, Y Gu, Z Liu, Q Long, Z Qiao, Y Qin… - Neural Networks, 2024 - Elsevier
Graph representation learning aims to effectively encode high-dimensional sparse graph-
structured data into low-dimensional dense vectors, which is a fundamental task that has …

Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review

VT Sabe, T Ntombela, LA Jhamba… - European Journal of …, 2021 - Elsevier
Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-
clinical drug discovery, and various computational techniques and software programs are …

Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

F Wong, A Krishnan, EJ Zheng, H Stärk… - Molecular systems …, 2022 - embopress.org
Efficient identification of drug mechanisms of action remains a challenge. Computational
docking approaches have been widely used to predict drug binding targets; yet, such …

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 learning force fields

OT Unke, S Chmiela, HE Sauceda… - Chemical …, 2021 - ACS Publications
In recent years, the use of machine learning (ML) in computational chemistry has enabled
numerous advances previously out of reach due to the computational complexity of …

Structure-based virtual screening: from classical to artificial intelligence

EHB Maia, LC Assis, TA De Oliveira… - Frontiers in …, 2020 - frontiersin.org
The drug development process is a major challenge in the pharmaceutical industry since it
takes a substantial amount of time and money to move through all the phases of developing …

Plant protein-derived antioxidant peptides: Isolation, identification, mechanism of action and application in food systems: A review

C Wen, J Zhang, H Zhang, Y Duan, H Ma - Trends in Food Science & …, 2020 - Elsevier
Background In recent years, the antioxidant capacity of plant protein-derived peptides has
been depicted in a growing number of studies. Plant proteins have been considered as the …

Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP …

FADM Opo, MM Rahman, F Ahammad, I Ahmed… - Scientific reports, 2021 - nature.com
X-linked inhibitor of apoptosis protein (XIAP) is a member of inhibitor of apoptosis protein
(IAP) family responsible for neutralizing the caspases-3, caspases-7, and caspases-9 …

Molecular docking: shifting paradigms in drug discovery

L Pinzi, G Rastelli - International journal of molecular sciences, 2019 - mdpi.com
Molecular docking is an established in silico structure-based method widely used in drug
discovery. Docking enables the identification of novel compounds of therapeutic interest …

Bioinformatics approaches to discovering food-derived bioactive peptides: Reviews and perspectives

Z Du, J Comer, Y Li - TrAC Trends in Analytical Chemistry, 2023 - Elsevier
Food-derived bioactive peptides (FBPs) are gaining interest due to their great potential in
agricultural byproduct valorization and high-activity peptide screening. The introduction of …