[HTML][HTML] A practical guide to large-scale docking

BJ Bender, S Gahbauer, A Luttens, J Lyu, CM Webb… - Nature protocols, 2021 - nature.com
Abstract Structure-based docking screens of large compound libraries have become
common in early drug and probe discovery. As computer efficiency has improved and …

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 …

Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity

AL Kaplan, DN Confair, K Kim, X Barros-Álvarez… - Nature, 2022 - nature.com
There is considerable interest in screening ultralarge chemical libraries for ligand discovery,
both empirically and computationally,,–. Efforts have focused on readily synthesizable …

AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings

J Eberhardt, D Santos-Martins… - Journal of chemical …, 2021 - ACS Publications
AutoDock Vina is arguably one of the fastest and most widely used open-source programs
for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks …

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 …

Physics-inspired structural representations for molecules and materials

F Musil, A Grisafi, AP Bartók, C Ortner… - Chemical …, 2021 - ACS Publications
The first step in the construction of a regression model or a data-driven analysis, aiming to
predict or elucidate the relationship between the atomic-scale structure of matter and its …

[HTML][HTML] A critical overview of computational approaches employed for COVID-19 drug discovery

EN Muratov, R Amaro, CH Andrade, N Brown… - Chemical Society …, 2021 - pubs.rsc.org
COVID-19 has resulted in huge numbers of infections and deaths worldwide and brought
the most severe disruptions to societies and economies since the Great Depression …

Machine-learning methods for ligand–protein molecular docking

K Crampon, A Giorkallos, M Deldossi, S Baud… - Drug discovery today, 2022 - Elsevier
Artificial intelligence (AI) is often presented as a new Industrial Revolution. Many domains
use AI, including molecular simulation for drug discovery. In this review, we provide an …

[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 …

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 …