[HTML][HTML] 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 …

Structure-based virtual screening for drug discovery: principles, applications and recent advances

E Lionta, G Spyrou, DK Vassilatis… - Current topics in …, 2014 - ingentaconnect.com
Structure-based drug discovery (SBDD) is becoming an essential tool in assisting fast and
cost-efficient lead discovery and optimization. The application of rational, structure-based …

Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation

S Keretsu, SP Bhujbal, SJ Cho - Scientific reports, 2020 - nature.com
In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing
drugs and evaluating commercially available inhibitors against druggable targets of the virus …

AtomNet: a deep convolutional neural network for bioactivity prediction in structure-based drug discovery

I Wallach, M Dzamba, A Heifets - arXiv preprint arXiv:1510.02855, 2015 - arxiv.org
Deep convolutional neural networks comprise a subclass of deep neural networks (DNN)
with a constrained architecture that leverages the spatial and temporal structure of the …

DOCK 6: Impact of new features and current docking performance

WJ Allen, TE Balius, S Mukherjee… - Journal of …, 2015 - Wiley Online Library
This manuscript presents the latest algorithmic and methodological developments to the
structure‐based design program DOCK 6.7 focused on an updated internal energy function …

Beware of docking!

YC Chen - Trends in pharmacological sciences, 2015 - cell.com
Docking is now routine in virtual screening or lead optimization for drug screening and
design. The number of papers related to docking has dramatically increased over the past …

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 …

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking

MM Mysinger, M Carchia, JJ Irwin… - Journal of medicinal …, 2012 - ACS Publications
A key metric to assess molecular docking remains ligand enrichment against challenging
decoys. Whereas the directory of useful decoys (DUD) has been widely used, clear areas for …

Machine and deep learning approaches for cancer drug repurposing

NT Issa, V Stathias, S Schürer… - Seminars in cancer …, 2021 - Elsevier
Abstract Knowledge of the underpinnings of cancer initiation, progression and metastasis
has increased exponentially in recent years. Advanced “omics” coupled with machine …

Recent advances in molecular docking for the research and discovery of potential marine drugs

G Chen, AJ Seukep, M Guo - Marine drugs, 2020 - mdpi.com
Marine drugs have long been used and exhibit unique advantages in clinical practices.
Among the marine drugs that have been approved by the Food and Drug Administration …