AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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 …
AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared …
Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets
WP Feinstein, M Brylinski - Journal of cheminformatics, 2015 - Springer
Background Computational approaches have emerged as an instrumental methodology in
modern research. For example, virtual screening by molecular docking is routinely used in …
modern research. For example, virtual screening by molecular docking is routinely used in …
Consensus docking: improving the reliability of docking in a virtual screening context
DR Houston, MD Walkinshaw - Journal of chemical information …, 2013 - ACS Publications
Structure-based virtual screening relies on scoring the predicted binding modes of
compounds docked into the target. Because the accuracy of this scoring relies on the …
compounds docked into the target. Because the accuracy of this scoring relies on the …
AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions
The performance of docking calculations can be improved by tuning parameters for the
system of interest, eg biasing the results towards the formation of relevant protein–ligand …
system of interest, eg biasing the results towards the formation of relevant protein–ligand …
InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening
Exploring protein–ligand interactions is a subject of immense interest, as it provides deeper
insights into molecular recognition, mechanism of interaction and subsequent functions …
insights into molecular recognition, mechanism of interaction and subsequent functions …
AUDocker LE: A GUI for virtual screening with AUTODOCK Vina
G Sandeep, KP Nagasree, M Hanisha, MMK Kumar - BMC research notes, 2011 - Springer
Background AUTODOCK Vina is an open-source program which is steadfast and authentic
to perform docking simulations. Though, Auto Dock Tools can help perform docking …
to perform docking simulations. Though, Auto Dock Tools can help perform docking …
DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0
Background Small-molecule docking is an important tool in studying receptor-ligand
interactions and in identifying potential drug candidates. Previously, we developed a …
interactions and in identifying potential drug candidates. Previously, we developed a …
rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids
S Ruiz-Carmona, D Alvarez-Garcia… - PLoS computational …, 2014 - journals.plos.org
Identification of chemical compounds with specific biological activities is an important step in
both chemical biology and drug discovery. When the structure of the intended target is …
both chemical biology and drug discovery. When the structure of the intended target is …
Accelerating AutoDock4 with GPUs and Gradient-Based Local Search
D Santos-Martins, L Solis-Vasquez… - Journal of chemical …, 2021 - ACS Publications
AutoDock4 is a widely used program for docking small molecules to macromolecular targets.
It describes ligand–receptor interactions using a physics-inspired scoring function that has …
It describes ligand–receptor interactions using a physics-inspired scoring function that has …
Dockey: a modern integrated tool for large-scale molecular docking and virtual screening
Molecular docking is a structure-based and computer-aided drug design approach that
plays a pivotal role in drug discovery and pharmaceutical research. AutoDock is the most …
plays a pivotal role in drug discovery and pharmaceutical research. AutoDock is the most …