[HTML][HTML] Molecular modeling in drug discovery

TI Adelusi, AQK Oyedele, ID Boyenle… - Informatics in Medicine …, 2022 - Elsevier
With the financial requirements and high time associated with bringing a commercial drug to
the market, the application of computer-aided drug design has been recognized as a …

[HTML][HTML] Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges

IA Guedes, FSS Pereira, LE Dardenne - Frontiers in pharmacology, 2018 - frontiersin.org
Structure-based virtual screening (VS) is a widely used approach that employs the
knowledge of the three-dimensional structure of the target of interest in the design of new …

Comparative assessment of scoring functions: the CASF-2016 update

M Su, Q Yang, Y Du, G Feng, Z Liu, Y Li… - Journal of chemical …, 2018 - ACS Publications
In structure-based drug design, scoring functions are often employed to evaluate protein–
ligand interactions. A variety of scoring functions have been developed so far, and thus …

Protein–ligand scoring with convolutional neural networks

M Ragoza, J Hochuli, E Idrobo, J Sunseri… - Journal of chemical …, 2017 - ACS Publications
Computational approaches to drug discovery can reduce the time and cost associated with
experimental assays and enable the screening of novel chemotypes. Structure-based drug …

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 …

Facile synthesis of copolymerized cellulose grafted hydrogel doped calcium oxide nanocomposites with improved antioxidant activity for anti-arthritic and controlled …

I Shahzadi, M Islam, H Saeed, A Shahzadi… - International Journal of …, 2023 - Elsevier
The combination treatment is considered an approach to attaining synergistic impact while
minimizing applied dosage. Hydrogels are analogous to the tissue environment attributed to …

Molecular docking: a powerful approach for structure-based drug discovery

XY Meng, HX Zhang, M Mezei… - Current computer-aided …, 2011 - ingentaconnect.com
Molecular docking has become an increasingly important tool for drug discovery. In this
review, we present a brief introduction of the available molecular docking methods, and their …

AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

O Trott, AJ Olson - Journal of computational chemistry, 2010 - Wiley Online Library
AutoDock Vina, a new program for molecular docking and virtual screening, is presented.
AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared …

Virtual chemical libraries: miniperspective

WP Walters - Journal of medicinal chemistry, 2018 - ACS Publications
Advances in computer processing speed and storage capacity have enabled researchers to
generate virtual chemical libraries containing billions of molecules. While these numbers …

Leveraging molecular structure and bioactivity with chemical language models for de novo drug design

M Moret, I Pachon Angona, L Cotos, S Yan… - Nature …, 2023 - nature.com
Generative chemical language models (CLMs) can be used for de novo molecular structure
generation by learning from a textual representation of molecules. Here, we show that hybrid …