A Rapid Approach to Generating a Protein-Ligand Costructure

Obtaining a protein-ligand structure is a critical component of a drug discovery project. Generally, X-ray crystallography and NMR are used to determine a high-resolution co-structure. But, this approach tends to be very time-intensive and is typically the limiting factor in a drug discovery process. Molecular modelling provides an extremely rapid alternative mechanism of generating a structure of a protein-ligand structure. Unfortunately, molecular docking methods suffer from common problems that include ambiguous ligand conformers or failure to predict the correct docked structure. AutoDockFilter provides a rapid approach to determine accurate protein-ligand costructures based on NMR chemical shift perturbations (CSPs) obtained from 2D ¹H-¹⁵N HSQC spectra in high-throughput ligand affinity screens. The CSP data is used to both guide and filter AutoDock calculations using our AutoDockFilter program.

AutoDockFilter is available as either a standalone python executable script or as an online service from our website. The standalone download, with usage instructions, is available below:

• ADF v2.0 source code

If you find AutoDockFilter useful, please cite the following manuscript:

• (63) J. Stark and R. Powers* (2008) "Rapid Protein-Ligand Costructures Using Chemical Shift Perturbations", J. Amer. Chem. Soc., 130(2):535-545. PMC18088118.

AutoDockFilter is open source and freely available for academic use. Industrial users may contact Robert Powers for licensing details.

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