A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

TN Jarada, JG Rokne, R Alhajj - Journal of cheminformatics, 2020 - Springer
Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs
and discovering therapies for untreated diseases. Drug repositioning, therefore, plays an …

Advancements in small molecule drug design: A structural perspective

K Wu, E Karapetyan, J Schloss, J Vadgama, Y Wu - Drug Discovery Today, 2023 - Elsevier
In this review, we outline recent advancements in small molecule drug design from a
structural perspective. We compare protein structure prediction methods and explore the …

The HDOCK server for integrated protein–protein docking

Y Yan, H Tao, J He, SY Huang - Nature protocols, 2020 - nature.com
Abstract The HDOCK server (http://hdock. phys. hust. edu. cn/) is a highly integrated suite of
homology search, template-based modeling, structure prediction, macromolecular docking …

SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration

D Idrees, V Kumar - Biochemical and biophysical research communications, 2021 - Elsevier
The post-infection of COVID-19 includes a myriad of neurologic symptoms including
neurodegeneration. Protein aggregation in brain can be considered as one of the important …

Molecular mechanism of evolution and human infection with SARS-CoV-2

J He, H Tao, Y Yan, SY Huang, Y Xiao - Viruses, 2020 - mdpi.com
The outbreak of a novel coronavirus, which was later formally named the severe acute
respiratory coronavirus 2 (SARS-CoV-2), has caused a worldwide public health crisis …

Improving peptide-protein docking with AlphaFold-Multimer using forced sampling

I Johansson-Åkhe, B Wallner - Frontiers in bioinformatics, 2022 - frontiersin.org
Protein interactions are key in vital biological processes. In many cases, particularly in
regulation, this interaction is between a protein and a shorter peptide fragment. Such …

SARS-CoV-2 proteins interact with alpha synuclein and induce Lewy body-like pathology in vitro

Z Wu, X Zhang, Z Huang, K Ma - International Journal of Molecular …, 2022 - mdpi.com
Growing cases of patients reported have shown a potential relationship between (severe
acute respiratory syndrome coronavirus 2) SARS-CoV-2 infection and Parkinson's disease …

CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function

Y Myung, DEV Pires, DB Ascher - Bioinformatics, 2022 - academic.oup.com
Motivation Understanding antibody–antigen interactions is key to improving their binding
affinities and specificities. While experimental approaches are fundamental for developing …

Protein–protein docking: Past, present, and future

S Sunny, PB Jayaraj - The protein journal, 2022 - Springer
The biological significance of proteins attracted the scientific community in exploring their
characteristics. The studies shed light on the interaction patterns and functions of proteins in …

Re-Exploring the Ability of Common Docking Programs to Correctly Reproduce the Binding Modes of Non-Covalent Inhibitors of SARS-CoV-2 Protease Mpro

D Bassani, M Pavan, G Bolcato, M Sturlese, S Moro - Pharmaceuticals, 2022 - mdpi.com
In the latest few decades, molecular docking has imposed itself as one of the most used
approaches for computational drug discovery. Several docking benchmarks have been …