A very recent paper, where the authors use an impressive combination of multiple docking programs (FlexX, eHiTS, Glide, AutoDock-Vina) and sub-terms of their scoring functions to identify new inhibitors of a Potassium Channel. It is also noteworthy that among all docking programs AutoDock-Vina achieved the best enrichment as shown by the ROC curves.
Wacker SJ, Jurkowski W, Simmons KJ, Fishwick CW, Johnson AP, Madge D, Lindahl E, Rolland JF, de Groot BL., "Identification of Selective Inhibitors of the Potassium Channel Kv1.1-1.2((3)) by High-Throughput Virtual Screening and Automated Patch Clamp.", ChemMedChem. 2012 Mar 30.
PMID: 22473914
AutoDock is a commercial-free suite of automated docking tools. Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina.
AutoDock has its own suite for receptor and ligand preparation:
http://mgltools.scripps.edu/
, as well as for Virtual Screening:
http://pyrx.sourceforge.net/
It has also been recently enriched with new scoring functions derived from neural networks:
http://www.nbcr.net/software/nnscore/
AutoDock can also be run in parallel on the web:
http://www.worldcommunitygrid.org/
https://www.nbcr.net/pub/wiki/index.php?title=CADD_Pipeline
There is also a bootable, self-configuring system for virtual screening, which can run AutoDock on multiple PCs that are not necessarily connected by a queueing system:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987878/
AutoDock has also its own PyMOL plugin:
http://wwwuser.gwdg.de/~dseelig/adplugin.html
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