Accelerating AutoDock Vina with GPUs [PDF]
Molecules, 2022 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 docking power among all the docking tools.
Shidi Tang, Ruiqi Chen, Yanxiang Zhu
exaly +4 more sources
High-Throughput, High-Quality: Benchmarking GNINA and AutoDock Vina for Precision Virtual Screening Workflow † [PDF]
MoleculesDrug discovery is an intricate and resource-intensive process in which computational approaches, such as molecular docking, are essential, particularly in the early stages, to identify potential hits.
Antonio Rescifina
exaly +4 more sources
Ecotoxicology and Environmental Safety, 2022 Molecular docking is a widely used method to predict the binding modes of small-molecule ligands to the target binding site. However, it remains a challenge to identify the correct binding conformation and the corresponding binding affinity for a series ...
Aiqian Zhang, Jianjie Fu, Xian Liu
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AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4 [PDF]
Biology Direct, 2020 AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates
Mario S. Valdés-Tresanco +3 more
doaj +2 more sources
An accurate and universal protein-small molecule batch docking solution using Autodock Vina
Results in Engineering, 2023 As an important theoretical computation method in computer-aided drug design, molecular docking has significantly shifted the paradigm of drug discovery.
Qilei Liu, Xinhao Che
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Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina [PDF]
PLoS ONE, 2010 The AutoDock family of software has been widely used in protein-ligand docking research. This study compares AutoDock 4 and AutoDock Vina in the context of virtual screening by using these programs to select compounds active against HIV protease.Both ...
Max W Chang, Bruce E Torbett
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Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening
Applied Sciences (Switzerland), 2019 AutoDock and Vina are two of the most widely used protein−ligand docking programs. The fact that these programs are free and available under an open source license, also makes them a very popular first choice for many users and a common starting ...
Tatiana F Vieira, Sérgio F. Sousa
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PeptoGrid—Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries [PDF]
Molecules, 2019 Peptides are promising drug candidates due to high specificity and standout safety. Identification of bioactive peptides de novo using molecular docking is a widely used approach.
Arthur O. Zalevsky +8 more
doaj +2 more sources
Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening. [PDF]
PLoS ONE, 2016 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).
Rodrigo Quiroga, Marcos A Villarreal
doaj +2 more sources
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings [PDF]
Journal of Chemical Information and Modeling, 2021 Andreas F. Tillack +2 more
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