Use of molecular docking computational tools in drug discovery

F Stanzione, I Giangreco, JC Cole - Progress in medicinal chemistry, 2021 - Elsevier
Molecular docking has become an important component of the drug discovery process.
Since first being developed in the 1980s, advancements in the power of computer hardware …

Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

Harnessing protein folding neural networks for peptide–protein docking

T Tsaban, JK Varga, O Avraham, Z Ben-Aharon… - Nature …, 2022 - nature.com
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …

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 …

From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2

H Bret, J Gao, DJ Zea, J Andreani, R Guerois - Nature communications, 2024 - nature.com
The revolution brought about by AlphaFold2 opens promising perspectives to unravel the
complexity of protein-protein interaction networks. The analysis of interaction networks …

Recent advance in tailoring the structure and functions of self-assembled peptide nanomaterials for biomedical applications

D Zhu, H Kong, Z Sun, Y Xu, P Han, Y **… - Coordination Chemistry …, 2023 - Elsevier
Molecular design and biomimetic/bioinspired synthesis provide facile ways for the
construction of functional nanomaterials for various applications. Peptide-based functional …

Highly flexible ligand docking: Benchmarking of the DockThor program on the LEADS-PEP protein–peptide data set

KB Santos, IA Guedes, ALM Karl… - Journal of Chemical …, 2020 - ACS Publications
Protein–peptide interactions play a crucial role in many cellular and biological functions,
which justify the increasing interest in the development of peptide-based drugs. However …

A comprehensive application: Molecular docking and network pharmacology for the prediction of bioactive constituents and elucidation of mechanisms of action in …

X Jiao, X **, Y Ma, Y Yang, J Li, L Liang, R Liu… - … Biology and Chemistry, 2021 - Elsevier
Traditional Chinese medicine (TCM) has been used for more than 2000 years in China.
TCM has received wide attention recently due to its unique charm. At the same time, its main …

Targeting endothelial vascular cell adhesion molecule-1 in atherosclerosis: drug discovery and development of vascular cell adhesion molecule-1–directed novel …

JR Pickett, Y Wu, LF Zacchi, HT Ta - Cardiovascular Research, 2023 - academic.oup.com
Vascular cell adhesion molecule-1 (VCAM-1) has been well established as a critical
contributor to atherosclerosis and consequently as an attractive therapeutic target for anti …

Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning

X Peng, Y Lei, P Feng, L Jia, J Ma, D Zhao… - Nature machine …, 2023 - nature.com
Computational modelling of the interactions between T-cell receptors (TCRs) and epitopes
is of great importance for immunotherapy and antigen discovery. However, current TCR …