Role of computer-aided drug design in modern drug discovery
Drug discovery utilizes chemical biology and computational drug design approaches for the
efficient identification and optimization of lead compounds. Chemical biology is mostly …
efficient identification and optimization of lead compounds. Chemical biology is mostly …
[HTML][HTML] Open source molecular modeling
The success of molecular modeling and computational chemistry efforts are, by definition,
dependent on quality software applications. Open source software development provides …
dependent on quality software applications. Open source software development provides …
Cryo-EM structure of the human cannabinoid receptor CB2-Gi signaling complex
Drugs selectively targeting CB2 hold promise for treating neurodegenerative disorders,
inflammation, and pain while avoiding psychotropic side effects mediated by CB1. The …
inflammation, and pain while avoiding psychotropic side effects mediated by CB1. The …
Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term
Scoring functions are important components in molecular docking for structure-based drug
discovery. Traditional scoring functions, generally empirical-or force field-based, are robust …
discovery. Traditional scoring functions, generally empirical-or force field-based, are robust …
Vinardo: A scoring function based on autodock vina improves scoring, docking, and virtual screening
R Quiroga, MA Villarreal - PloS one, 2016 - journals.plos.org
Autodock Vina is a very popular, and highly cited, open source docking program. Here we
present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based …
present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based …
Accelerating autodock vina with gpus
AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark
CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best …
CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best …
Large-scale prediction of binding affinity in protein–small ligand complexes: The PRODIGY-LIG web server
Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the
prediction of binding affinity in protein–protein complexes. By using a combination of simple …
prediction of binding affinity in protein–protein complexes. By using a combination of simple …
Vina-GPU 2.0: further accelerating AutoDock Vina and its derivatives with graphics processing units
J Ding, S Tang, Z Mei, L Wang, Q Huang… - Journal of chemical …, 2023 - ACS Publications
Modern drug discovery typically faces large virtual screens from huge compound databases
where multiple docking tools are involved for meeting various real scenes or improving the …
where multiple docking tools are involved for meeting various real scenes or improving the …
A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function
The recently reported machine learning-or deep learning-based scoring functions (SFs)
have shown exciting performance in predicting protein–ligand binding affinities with fruitful …
have shown exciting performance in predicting protein–ligand binding affinities with fruitful …
Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors
A Jimenez-Alberto, RM Ribas-Aparicio… - … biology and chemistry, 2020 - Elsevier
The global emergency caused by COVID-19 makes the discovery of drugs capable of
inhibiting SARS-CoV-2 a priority, to reduce the mortality and morbidity of this disease …
inhibiting SARS-CoV-2 a priority, to reduce the mortality and morbidity of this disease …