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How to prep your ligand for Autodock?

Searching the conformational space for docking

Ligand (biochemistry)

Docking (molecular)

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Journal Article•DOI Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. Robin J. Rosenfeld, David S. Goodsell, Rabi A. Musah, Garrett M. Morris, David B. Goodin, Arthur J. Olson - Show less +5 more 01 Aug 2003-Journal of Computer-aided Molecular Design 93 Citations	In summary, AutoDock 3.0 appears to be useful in predicting key structural and energetic features of ligand binding in the W191G cavity.
Journal Article•DOI A comparative docking study and the design of potentially selective MMP inhibitors. Stephen Hanessian, Nicolas Moitessier, Eric Therrien - Show less +2 more 01 Oct 2001-Journal of Computer-aided Molecular Design 26 Citations	AutoDock proved to be highly reliable, efficient and predictive for a set of inhibitors with less than six atom types.
Journal Article•DOI Modified AutoDock for accurate docking of protein kinase inhibitors. Oleksandr V. Buzko, Anthony C. Bishop, Kevan M. Shokat - Show less +2 more 01 Feb 2002-Journal of Computer-aided Molecular Design 54 Citations	In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations. However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38.
Journal Article•DOI Parallel implementation of AutoDock Prashant Khodade, R. Prabhu, Nagasuma Chandra, Soumyendu Raha, Ramaswamy Govindarajan - Show less +4 more 01 Jun 2007-Journal of Applied Crystallography 44 Citations	This implementation would make it feasible to perform virtual ligand screening using AutoDock.

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What is autodock4?4 answersAutoDock4 is a widely used program for docking small molecules to macromolecular targets. It uses a physics-inspired scoring function to describe ligand-receptor interactions and has been proven useful in drug discovery projects. However, AutoDock4 has longer execution times compared to more modern software, limiting its applicability to large-scale dockings. To address this issue, an OpenCL implementation of AutoDock4 called AutoDock-GPU has been developed, which leverages the parallel architecture of GPU hardware to significantly reduce docking runtime. AutoDock4 has also been used in docking simulations to identify inhibitors of the main protease of SARS-CoV-2 (Mpro), the causative agent of COVID-19. These studies have found potential inhibitors of Mpro with estimated inhibition in the nanomolar range, although some of them lack proper validation of the docking protocol. AMDock is a user-friendly graphical tool that assists in the docking of protein-ligand complexes using AutoDock4, offering several alternatives and different degrees of user supervision. Autodock4 has been found to perform well in absolute binding free energy predictions, outperforming expensive molecular dynamics or quantum chemistry techniques in some instances.

What tools can use for protein ligand docking ?3 answersProtein-ligand docking can be performed using various tools. One such tool is FitDock, which utilizes a hierarchical multi-feature alignment approach to fit initial conformations to given templates and explore possible conformations for docking poses. Another tool is HCovDock, which is specifically designed for covalent protein-ligand interactions and integrates ligand sampling and scoring functions with covalent bond-based energy. CB-Dock2 is an updated docking server that combines template-based docking with blind docking to enhance accuracy in binding site identification and binding pose prediction. Additionally, protein-based docking programs such as FRED, HYBRID, and FlexX have been shown to perform well in reproducing native binding modes of small molecule RNA ligands and discriminating known binders from decoys. These tools provide valuable resources for protein-ligand docking in drug design and structural bioinformatics.

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