AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
By Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson. 2009
23,062 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Infectious Diseases, Virology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Computational Theory and Mathematics
- John Karanicolas
- Stefano Forli
- Vincent Zoete
- Olivier Michielin
- Brian K. Shoichet
- Antoine Daina
- Elizabeth Yuriev
- Paul A. Ramsland
In Infectious Diseases
- Stefano Forli
- Abdo A. Elfiky
- John Karanicolas
- David S. Goodsell
- Ruben Abagyan
- Arthur J. Olson
- Michel F. Sanner
- G. Wei
In Virology
- Stefano Forli
- Abdo A. Elfiky
- John Karanicolas
- David S. Goodsell
- Ruben Abagyan
- Arthur J. Olson
- Michel F. Sanner
- Shengyou Huang
Citations in the corpus
- A perspective on multi-target drug discovery and design for complex diseases (2018, methodology): “The most often used docking software packages are CDOCKER [65], GOLD [66] and AutoDock [67].”
- Computer-Aided Drug Design Methods (2017, methodology): “Additional scoring metrics can include the DOCK or AUTODOCK scores (49, 50), or the average interaction energies from MD simulations, with many other variations available. are selected from this round based on the vdW attractive energy normalized for the compound molecular weight (81).”
- Toward prediction of functional protein pockets using blind docking and pocket search algorithms (2011, methodology): “The RMSD of Rank 1 (Supporting Information) was an excellent 0.9 A˚ with AutoDock4 18,19 and 2.6 A˚ using EADock.”
- Protein-Ligand Interaction Graphs: Learning from Ligand-Shaped 3D Interaction Graphs to Improve Binding Affinity Prediction (2022, methodology): “They are used in popular docking software such as AutoDock4 ([2, 3]), AutoDock Vina ([4]) or GOLD ([5]) to score 3D ligand poses.”
- SwissTargetPrediction: a web server for target prediction of bioactive small molecules (2014, background): “To address such issues, one possibility is to use other orthogonal computational approaches, such as structure-based analyses or molecular docking (44,45), to refine the predictions by considering small changes in protein binding sites that could confer specificity to some targets.”
- AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4 (2020, methodology): “…of available GUIs (developed mostly for AutoDock [1] and/or Autodock Vina [2]) are AutoDock Tools (ADT), integrated into the PMV graphical package [1], BDT [3], DOVIS [4, 5], VSDocker [6], AUDocker LE [7], WinDock [8], DockoMatic [9], PyMOL AutoDock plugin (PyMOL/AutoDock) [10], PyRx [11], MOLA…”